Mets Minors: Updated Top 10 list

With the Mets seemingly on the verge of a salary purge over the next few months and going to have to rely on the farm system more over the next several years, let’s look at an updated top-10 prospect list for the embattled organization.

The farm system lacks top-end talent and depth. Injuries this season have thwarted the progress of top pitcher Jenrry Mejia, infielders Zach Lutz and Reese Havens and outfielders Darrell Ceciliani and Fernando Martinez, who hasn’t been able to stay healthy or reach his potential. Havens has just returned from his latest injury, but he has to be considered more suspect than prospect at this point.

Slow starts have also impacted outfielders Cesar Puello and Lucas Duda, third baseman Aderlin Rodriguez and pitchers Brad Holt, Robert Carson and Kyle Allen. The Mets don’t have a legitimate catching prospect in the system, and, if Wilmer Flores moves from shortstop, the organization doesn’t have a legit everyday prospect in the middle of the infield, just several utility types: Havens, Justin Turner, Michael Fisher, Josh Satin, Jordany Valdespin and Robbie Shields.

On the positive side, Matt Harvey and Jeurys Familia have established themselves as top prospects, Kirk Nieuwenhuis has shown he’s an everyday player in the big leagues and youngster Cory Vaughn continues to hit. Class AA first baseman Allan Dykstra has been a pleasant surprise along with Class A center fielder Matt den Dekker.

“Sleeper” pitchers include AAA hurlers Chris Schwinden and recently-promoted Dale Thayer, high Class A lefthander Darin Gorski and low Class A righthander Gregory Peavey.

Below are the top-10 prospects in the Mets’ organization. Qualifications: Fewer than 100 plate appearances or 50 innings pitched in the major leagues prior to this season.

1. Matt Harvey

Other than two shaky outings, Harvey has been sensational in his pro debut season, and with the injury to Mejia, he has taken over the top spot on the mound.

The 2010 first-round pick from North Carolina is 6-2, with a 2.50 ERA and 1.17 WHIP in his first 10 starts. He’s allowed 45 hits and 18 walks in 54 innings with 62 strikeouts. The righthander has allowed no earned runs in seven of his 10 outings.

Harvey’s got the heat, command, pedigree, projectable body and offspeed stuff to be a staff ace.

2. Kirk Nieuwenhuis

There is very little doubt Nieuwenhuis will find himself playing regularly in New York once the financially strapped Mets start dumping salary.

Nieuwenhuis began the season with a 16-game hitting streak and has showed signs of making adjustments. The 23-year-old is batting .302/.407/.521 after a .225 average in 30 games for Buffalo last season. He has 15 doubles, two triples, six homers, 14 RBI, 29 walks and five steals in 47 games.

Nieuwenhuis is making strides against fellow lefthanders – .235 but 11 walks in 51 AB – but still needs to cut down on his strikeouts – 51 in 169 at-bats – and is batting just .182 with runners in scoring position. The center fielder is the only player in the International League to play in every game, and he is getting time in right field as well.

3. Wilmer Flores
Although Flores will probably outgrow shortstop, the 6-foot-3 righthanded batter is a potential hitting machine.

A recent slump has dropped his average to .267/.305/.381with 11 doubles, four homers and 35 RBI in the pitcher-friendly Class A Florida State League, but he has just 10 walks in 202 at-bats. But Flores won’t turn 20 until August and is playing against players 22 to 24 years of age.

His range is suspect at shortstop, so third base or a corner outfield spot probably awaits, but Flores has committed just six errors in 50 games.

4. Cory Vaughn

Vaughn is looking like the complete offensive package at low Class-A Savannah, batting .335/.466/.483 in 50 games with 14 doubles, four homers and 26 RBI.

The just turned 22-year-old also has 31 walks and 43 strikeouts in 176 at-bats, and he has stolen eight bases. Vaughn was a New York- Penn League All-Star last season and posted a .953 OPS so look for the righthanded hitter to move on to St. Lucie for the second half of the season.

5. Jenrry Mejia

Mejia unquestionably has the biggest upside of any Mets hurler with a “plus-plus” fastball that could either front a rotation or close out a game at the back. But the 21-year-old has just lost a second straight year of development when he blew out his elbow in late April after going 1-2 with a 2.86 ERA and 1.06 WHIP in five starts.

After undergoing Tommy John surgery, Mejia now faces a long rehabilitation stint – nine to 12 months. Prior to the season, Mets pitching coach Dan Warthen questioned whether Mejia and his all-out delivery would hold up as a starter.

6. Jeurys Familia

Along with Harvey, the 21-year-old Familia has been the best pitcher in the organization this season.

Familia is 0-1 with a 2.25 ERA and 1.13 WHIP in four starts for offensively-challenged Binghamton after going 1-1 with a 1.49 ERA and a 0.80 WHIP at St. Lucie.

The 6-foot-3 righthander with a mid-90s heater is no doubt the best one-win hurler in the minors, allowing 39 hits and 17 walks with 57 strikeouts in 60 1/3 innings. An off-the-charts improvement in command is the biggest reason Familia has been able to bounce back from 5.58 ERA at St. Lucie a season ago.

7. Pedro Beato

The 24-year-old has been a pleasant surprise in the middle of the bullpen.

Beato began the season without allowing an earned run in his first 12 outings covering 18 2/3 innings. Only Oakland reliever Brad Ziegler’s career-opening streak of 38 innings in 2008 is longer to start a career than Beato’s since 2000. The Brooklyn product yielded just nine hits, three walks and four unearned runs during that span with 11 strikeouts.

A bout with elbow tendinitis landed the Rule V pick from the Baltimore Orioles on the DL the first three weeks of May, and the righthander has been tagged for seven runs and eight hits in four innings over his last four outings.

The 6-6 Beato was a mediocre starter his first four years in the minors before switching to the pen, posting a 2.11 ERA and 16 saves at Class AA Bowie last season, walking 19 and striking out 50 in 60 innings. He doesn’t have overpowering heat and his offspeed pitches are still developing.

8. Matt Den Dekker

Already a major league-ready center fielder, Den Dekker has impressed the brass with a .315/.359/.502 out of the leadoff spot for St. Lucie.

The 23-year-old can run as his 16 doubles, eight triples and nine steals would indicate, and he’s added two homers and 27 RBI in 49 games. The 2010 fifth-rounder from the Univeristy of Florida is batting .328 against fellow lefthanders but will need to improve upon his 13/46 BB/SO ratio over 203 at-bats to play every day.

9. Dillon Gee

Does anybody believe in Dillon Gee yet?

Nobody did after the velocity-challenged righthander went 2-2 with a 2.18 ERA and 1.21 WHIP in five major league starts last season, but Gee is 5-0 with 3.83 ERA and 1.15 WHIP in 10 games – seven starts – for New York this season.

His lack of velocity and past results suggest the 25-year-old may be using smoke and mirrors, but its time Gee gets the props he deserves.

10. Cesar Puello

The 20-year-old is a “tools” player who is more potential than productivity at this point, but scouts can’t ignore his 6-3, 200-pound athletic frame, outstanding speed and power potential.

The Dominican is struggling against more-seasoned players in the Florida State League, batting .234/.288/.328 with two homers, 11 RBI and 10 steals in 46 games. His nine walks and 43 strikeouts in 192 at-bats will have to improve.

*****

Here is our preseason Top 10

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The Cory Vaughn story

Greg Vaughn hit 355 home run in his major league career, including 11 against the New York Mets. He was a four-time All-Star and surpassed 30 home runs four times in his 15-year career.

His son Cory has one spring training homer for the Mets, but New York hopes that he’ll hit a lot more for the big club starting in a few years.

Vaughn, a fourth-round draft pick last year out of San Diego State where he played for Hall of Famer Tony Gwynn, had an eye-opening debut summer season for Brooklyn in the Class A New York – Penn League.

He showed the power-speed combination his father possessed, hitting .307/.396/.557 in 72 games for the Cyclones as a 21-year-old. The right-handed hitter had 14 doubles, five triples, 14 homers and 56 RBI in 72 games with 34 walks and a rather-high 63 strikeouts. He was successful on 12-of-17 stolen base attempts and led the league in slugging and OPS (.953) while ranking second in homers and RBI.

The younger Vaughn is built like his father at 6-3 and 225 pounds, has power potential and will be a plus-hitter if he can stay away from breaking balls and curb his strikeouts.

Vaughn hit .378 with team highs of nine homers and 55 RBI in his junior season at San Diego State under Gwynn and cut down on his swing after turning pro. Scouts say Vaughn plays a decent corner outfield spot – he played right for Brooklyn – and has an average arm.

In addition to his father and playing under Gwynn, whom his father played with from 1996-98, Vaughn played with Washington Nationals pitching phenom Stepen Strasburg in college.

“We played him in the fall,” Vaughn told ESPN.com last summer “I got him once or twice, but he got me the other times. But it was a great battle. Not take him deep, but I squared him up a few times. Not too many. It was challenging, and I like that. It made me better a little bit to see some good stuff.”

Vaughn will have one other challenge to overcome; he is a diabetic and monitors with an insulin pump while he plays.

“Coach Gwynn, the first thing he says to me, he goes, ‘Hey, there’s no cell phones or MP3 players on the field,’” Vaughn told ESPN.com. “The first day I went out to practice, because I’m diabetic and I wear an insulin pump, I had the pump in my back pocket, and it’s connected to me. I’m like, ‘No coach. I’m diabetic. This is my stuff.’ He’s like, ‘Oh, oh.’”

As for his Type 1 (juvenile) diabetes, which leaves his body unable to self-regulate its blood sugar levels, Vaughn has dealt with the condition since being diagnosed at 11 years old.

“You’ll see it in my pocket. It’s like a little pump,” Vaughn said of the apparatus he carries with him, even during games. “I stick a needle in my thigh. And I take the needle out, and there’s like a little catheter in me and it just pumps insulin every hour.

“It is what it is. Either I do it, or it’s not going to be any good. It really wasn’t an obstacle. I just took it as a mountain I had to climb. I’ve been doing very well at it.”

Vaughn is in the process of scaling the mountain to the major leagues as well.

Mets 2011 Top 10 Prospects

One of the reasons cited for getting rid of Omar Minaya was that he did not build a strong farm system. Last year, six players who made my top prospect list contributed to the Mets and no longer have rookie eligibility. This includes Jenrry Mejia and Fernando Martinez, both who lost their rookie status because they accumulated more than 45 days on the active roster.

So, it is actually surprising the overall shape of the system. There’s not much at the very top, but there is a lot of depth, a lot of players who could eventually reach the majors. At this time last year, few would have guessed that Mejia, Ike Davis and Ruben Tejada would have used up their eligibility. If those three were still rookies and had turned in strong 2010 seasons in the minors (not an unreasonable assumption), the outlook of the Mets’ farm system would be completely different right now.

As is, there are some hitters who may top out as reserves but who still have time to develop into useful regulars. The top pitchers now in the system are Matt Harvey and Steven Matz; unfortunately, neither one of them has thrown a pitch in professional baseball and ranking them is extremely problematic.

Only four players return from last year’s list. There may only be four people from the 2011 list who show up on the 2012 list, too. But unlike last year, when everyone graduated to the Mets or lost their eligibility, next year’s list might have a lot of turnover just because there are 15-17 people who can make an argument to be on the list right now. With another year of data and scouting reports, people who missed the list this time could easily take a step forward.

10. Reese Havens, 2B, Hi-A/Double-A, .338/.400/.662 in 75 PA

This is Havens’ line in Double-A, where he actually played more than he did in Single-A. And this illustrates both the potential and the problem with Havens. He has an impact bat at second base. But he can’t stay healthy. As Mets fans have seen with Martinez, staying healthy is at least partially a skill. Havens has been injured in each of his three years with the Mets. Most people have Havens ranked higher than this in the system. He’s this low here because until he stays healthy he’s more suspect than prospect. He could be number one on this list next year. Or he could fall off completely.

9. Lucas Duda, OF/1B, Double-A/Triple-A/Majors, .314/.389/.610 in 298 PA

This is Duda’s line in Triple-A, when he had 42 XBH, including 17 HR. Duda saw extensive playing time with the Mets in September. He couldn’t buy a base hit his first two weeks in the majors. But in his final 55 PA, he put up a .314/.345/.647 line with 9 XBH and 4 HR. Duda has big-time power. The issue is: Where is he going to play? He played LF with the Mets in September, but that position is manned by Jason Bay. His best position is 1B, but Davis has a leg up there. Potentially, RF could be his home, but Duda was already stretched defensively in LF. In his brief action in the majors, he was below average in both range and arm. Again, Duda is a player that most others rank higher. My problem is that I just don’t see where he fits on the Mets.

8. Dillon Gee, SP, Triple-A, Majors, 13-8, 4.96 ERA, 165 Ks in 161.1 IP

Last year Gee made my list ahead of Brad Holt and Jeurys Familia. The rationale was that he had less upside but was more likely to pitch in the majors. Right now, Gee is the Mets’ fourth starter. Whether he’s in the rotation on Opening Day or not, Gee is likely to pitch again in the majors in 2011. His stuff is not good enough to be a guy to make 30 starts a year. But he could make it as a swing man or a bullpen arm.

7. Matt Harvey, SP, UNC, 8-3, 3.09 ERA, 102 Ks in 96 IP

The seventh overall pick in the 2010 Draft, Harvey had one of the best fastballs in the draft. The question is if he has anything else. Some compare him to Mike Pelfrey, but Pelfrey had better control than Harvey in college. In an ordinary year, Harvey would probably not make this list. But he clearly has upside, and unlike Matz, is not coming off surgery. We should get a better reading on Harvey after this year and I expect he’ll move up on the list.

6. Darrell Ceciliani, OF, New York-Penn League, .351/.410/.531 in 303 PA

A fourth-round pick in the 2009 Draft out of a Junior College in Washington, Ceciliani rebounded from a poor year in his professional debut in the APPY to put up a very fine last year, especially for a center fielder. In addition to winning the batting title, Ceciliani had 33 XBH in 271 ABs, which broke down to 19 doubles, 12 triples and 2 homers. If he can stay in center field, Ceciliani has a chance. He has little power and not much arm, so he needs to stay in center in order to be a starter. He’s a long way from the majors but he has legitimate tools. We’ll find out how legitimate when he plays in full-season ball this year.

5. Kirk Nieuwenhuis, OF, Double-A/Triple-A, .289/.337/.510 in 433 PA

This is Nieuwenhuis’ line in Double-A. He struggled in 30 games in Triple-A but it was still a successful season for the former small college star. Nieuwenhuis was leading the Eastern League with 53 XBH when he was promoted. The big issue is if, like Ceciliani, he can stay in center. Last year I compared him to Nate McLouth, a guy stretched to play CF, but one capable of putting up a 20-20 line. There are doubts about Nieuwenhuis because of his NAIA pedigree. But he’s gotten better as he’s moved up the ladder and I’m going to believe in him until he gives me a reason not to.

4. Cesar Puello, OF, South Atlantic League, .292/.375/.359 in 469 PA

The Dominican native was signed by the Mets in 2007. Last year was his third season playing in this country but he was only 19, one of just five teenagers in the SAL. Unlike many Latin players, Puello is willing to take a walk, with 32 BB in 404 AB,. Puello also had 22 HBP, following up on a season where he was hit 14 times in short-season ball. He also has plus speed, as he stole 45 bases in 55 attempts. Puello hit just 1 HR last year, but he draws praise for his approach at the plate and scouts predict he will hit 20 HR by the time he matures.

Despite his speed, Puello is a right fielder. On production, Nieuwenhuis is the better prospect right now. But Puello has a higher ceiling. It is a coin flip for me which one to rank higher and I am tempted to flip the coin again and put Nieuwenhuis in this spot. Ultimately, Puello gets the nod. He should advance to the Florida State League next year, a tough league for youngsters to hit home runs. Puello may not show much improvement in power next season but let’s see if his plate discipline holds at the higher level.

3. Aderlin Rodriguez, 3B, Rookie/Low-A, .312/.352/.556 in 267 PA

This is Rodriguez’ line in the Appalachian League. He got a late call-up to the SAL, where he played in eight games. While he is a year behind Puello, and with only eight games of full-season ball to his credit, Rodriguez is ranked higher due to greater power production and potential, along with his chance to stick in the infield. Rodriguez bounced back from a wrist injury in 2009 to put up 13 HR in 250 ABs in the APPY, which ranked third in the league.

The Dominican native shows a strong arm at the hot corner, but scouts worry about every other defensive tool for Rodriguez. He may have to move to first base but should have the bat for the position. There have been whispers about his work ethic, which is a concern, but let’s see if they follow him to full-season ball before we give them too much weight.

2. Cory Vaughn, OF, New York-Penn League, .307/.396/.557 in 313 PA.

The Mets’ fourth-round pick in the 2010 Draft out of San Diego State, Vaughn is the son of former MLB star Greg Vaughn. The younger Vaughn had a big year in the NYP, hitting for both average and power (14 HR) while also showing the speed to steal 12 bases. While a rookie league, the NYP is the natural spot for many college players and first-round picks. Under the old Mets regime, Vaughn would likely have opened 2011 in Double-A. Now, he’s likely headed to the Hi-A Florida State League, instead.

Vaughn has Type I juvenile diabetes, a condition he has had since he was 11. He tests himself multiple times during a game. So far the condition has not been a hindrance in any way in his baseball development. Vaughn has benefitted from being around the game his entire life. He was in the clubhouse when was his father was in San Diego and a teammate of current SDSU coach Tony Gwynn. He was also a bat boy later on when his father was in Tampa Bay.

Some doubt Vaughn as he did not impress in the Cape Cod League and never hit a lot of HR at SDSU, either. But Vaughn’s showing in the NYP should silence some of the critics. If he again hits for average and power in 2011, expect to see Vaughn’s name on MLB top prospect lists this time next year. But right now this is probably the highest ranking you will see for Vaughn anywhere.

1. Wilmer Flores, SS, Low-A/Hi-A, .278/.342/.433 in 307 PA

These are the numbers for Flores in the South Atlantic League, where he played the first half of 2010. He hit for a better average (.300) in the Florida State League, but with less OBP and SLG. Flores improved upon 2009’s dismal numbers in the SAL but his top prospect status is still built more upon age, as he was 18 for most of last season, than on production.

While listed as a SS, few expect he will play that position in the majors. Flores has good hands, but does not have the range of an MLB-quality shortstop. His likely home is third base. But wherever he winds up defensively, Flores’ value will come from his bat. The Venezuelan native makes good contact (77 Ks in 554 ABs in 2010) and hits the ball to all fields.

Flores is likely to start the year in the FSL, with a mid-year promotion to Double-A. Not many people are capable of playing in the high minors while still a teenager. It is easy to get down on Flores, as his production has yet to match his hype. But no one should be surprised once he starts to put up big numbers. Nor should they be shocked if that happens in 2011.

Honorable Mention/Names to Remember

Holt, Familia, Matz, Jordany Valdespin, Mark Cohoon, Zach Lutz, Robert Carson, Matt den Dekker, Jefry Marte, Juan Urbina, Vicente Lupo, Elvis Sanchez.

2010 Top Prospects
2009 Top Prospects

Mets Draft Update

Monday plans on being a busy day for the Mets.

The deadline to sign draft picks is 11:59 pm and the club has yet to sign righthanded pitcher Matt Harvey, the seventh overall pick and a junior from North Carolina. Harvey was 8-3 with a 3.09 ERA this spring with 35 walks and 102 strikeouts in 96 innings.

Adding to the drama will be Harvey’s agent – Scott Boras, but mlb.com is reporting the Mets “feel good about being able to get him signed by the time the deadline hits.”

New York did not have a second-round pick, but each of its next three picks is playing in Class A Leagues. Sixth-round selection, righthander Greg Peavey, who was 6-3, 3.64 ERA in 15 starts at Oregon State, also has not signed and could return to school.

Below is a look at how some of the Mets top draft picks from previous seasons are faring this season.

2010 Draft

Third round – Catcher Blake Forsythe is batting .257/.317/.365 with a homer, four RBI and 26 strikeouts in 74 at-bats combined at the rookie-level Gulf Coast League and Class A New York – Penn.

Fourth round – Center fielder Cory Vaughn is batting .316/.402/.569 with 12 homers, 44 RBI and 10 steals at Brooklyn. The 21-year-old product of San Diego State and the son of former major league slugger Greg Vaughn is tied for the league lead in RBI, is second in homers and third in slugging.

Fifth round – Center fielder Matt Den Dekker played five games in the Gulf Coast League before moving to low Class-A Savannah where he has gone 11-for-28 with six RBI in his first six RBI. He is known for his outstanding defense.

2009 Draft

First round – Did not have a first-round pick.

Second round – Lefthander Steven Matz is out for the season after undergoing Tommy John elbow surgery on May 18. The 19-year-old has not pitched in his first two years of professional baseball.

Third round – Shortstop Robbie Shields returned from TJ surgery in June and is batting .257/.307/.371 in stints in the Gulf Coast, South Atlantic League and Florida State League.

Fourth round – Center fielder Darrell Ceciliani is having a great season at Class A at Brooklyn. The 20-year-old is leading the league in batting (.371), triples (10), hits (82), and runs (47), is second in OPS (.972), third in doubles (16), fourth in steals (18) and fifth in slugging (.548). The lefthanded hitter has a homer and 28 RBI in 56 games.

Fifth round – Righthander Damien Magnifico did not sign.

Sixth round – Righthander David Buchanan did not sign.

2008 Draft

First round – First baseman Ike Davis is batting .248/.324/.420 with 15 homers and 54 RBI in 101 games with New York. The lefthanded hitter started with Class AAA Buffalo, batting .264/.500/.636 with a pair of homers in 10 games.

First round – Second baseman Reese Havens is hitting .312/.386/.592 between Class A and AA, but the converted shortstop has not played since June 11 because of a strained oblique.

First round (supplemental) – Righthander Brad Holt is 3-11, 7.83 ERA with a 1.941 WHIP at Class A and AA.

2007 Draft

First round supplemental – Lefthander Eddie Kunz is 6-7 with a 5.23 ERA at Class AA in 35 games – nine starts.

First round supplemental – Lefthander Nathan Vineyard is out of baseball after two injury-filled seasons.