General manager Omar Minaya has come under a lot of fire for not having more prospects in the farm system ready to step in and contribute when the Mets were hit by all of the injuries last year. There is some validity to that criticism. However, given the condition of the Mets farm system when Minaya took over, the trades of prospects to acquire Johan Santana and J.J. Putz and the team frequently forfeiting its top draft choices to sign Type A free agents, the Mets’ system is in surprisingly good shape.

There are a couple of impact-type players, people with a chance to contribute on a good team and prospects whose main value may come as trade chits. Also, there is more organizational depth than in years. While it is still not one of the top systems in the game, it is in the top half and might even sneak into the bottom of the top third of all farm systems in the majors.

Recently, the Mets had an organizational philosophy of aggressively challenging their top prospects, to see how they would handle failure. This ended up with players at levels way above where their age and talent would normally dictate. The results have not been especially impressive (Ruben Tejada last year a noticeable exception) and it will be interesting to see if this continues now that Tony Bernazard is no longer with the organization.

We should find out right away if there is any change in philosophy. Where will Wilmer Flores and Jefry Marte, two youngsters who struggled in their first exposure to full-season ball, start the year? Ordinarily, we might expect both of them to be in the Hi-A Florida State League, given the team’s aggressive nature. However, they both should repeat the Low-A South Atlantic League, where they still will be young for the league.

Here is how I view the top prospects in the system. The ranking is based primarily on long-term potential impact but a player who has reached Double-A or higher does receive an extra bit of credit. Ranking prospects is as much of an art as it is a science. Everybody has to decide for themselves where they place a player like Flores, who has a world of talent but is several levels away from the majors, compared to a Josh Thole, who has a much lower ceiling, but one who has already played in the majors.

10. Dillon Gee, RHP, International League, 1-3, 4.10 ERA, 42 Ks, 48.1 IP.

Gee would have been in line for a promotion last year but his season ended early with a shoulder injury. The numbers do not look overly impressive but Gee did have a Quality Start in three of his last four games before the injury. He’s not overpowering but he has good control, gets his fair share of grounders and keeps the ball in the park. Gee also holds his own versus LHB. Lefties hit .256 against him last year and have a lifetime .262 AVG against the soon-to-be 24-year old. Both Brad Holt and Jeurys Familia have higher ceilings than Gee but Gee is on the cusp of the majors and may make it as a starter. This time next year it may seem silly to think Gee as more valuable than Holt and Familia. It’s a minority opinion right now. But Holt had a 6.12 ERA in Double-A and Familia needs to prove his stuff will work above Low-A.

9. Kirk Nieuwenhuis, OF, Florida State League/Eastern League, .274/.357/.467

He had 51 XBH in 482 ABs in the FSL and his ISO of .193 tied for the league lead in the pitching-heavy loop. Nieuwenhuis went to an NAIA school so he did not receive the hype of a typical Division I prospect. But he has good power, he can run and he is a good defensive outfielder, capable of playing CF although he may spot better in a corner. If he continues to develop and everything falls right, Nieuwenhuis could be a .250/.350/.450 guy in the majors with 20-HR, 20-SB potential. That’s pretty much the definition of Nate McLouth.

8. Reese Havens, SS, Florida State League, .247/.361/.422

Unlike Nieuwenhuis, Havens went to South Carolina and therefore is considered a better prospect. He definitely has a position advantage, although he will not play SS in the majors. Another hallmark of the Bernazard-era Mets was to leave guys at a premium defensive position as long as possible, even if everyone agreed his future home was elsewhere. David Wright was a high school SS but everyone knew he would become a 3B and the Mets quickly moved him so he could get familiar with his new position. Havens is really a 2B. He has not hit for AVG yet but has showed good on-base and power skills. The other problem has been injuries. Havens needs a healthy season where he hits over .250 or else he will fall off this list completely.

7. Ruben Tejada, SS, Eastern League, .289/.351/.381

As an 18-year old in the FSL, Tejada had a .589 OPS. A year later in Double-A he had a .732 OPS which is just a tremendous improvement. He is never going to hit for power but if he can continue to hone his OBP skills he is going to be a regular in the majors. Assuming the Mets retain Reyes, he will battle Havens for the right to be the starter at 2B. But even if Havens reaches his ceiling and wins the job, Tejada will make a good utility player. Tejada simply has a higher floor than Havens and his upside is 2002-05 era Luis Castillo, who was a 3.5 WAR player.

6. Josh Thole, C, Eastern League/Majors, .321/.356/.396

No one wants to admit the obvious – Thole is going to be a major league catcher, and the sooner that happens the better. People focus on what he (allegedly) cannot do rather than what he brings to the table. A catcher who can hit .300 with a .350 OBP and throw out 20 percent of runners is an asset. No, he is not going to hit for any power. No, he is not going to win Gold Gloves.

But let’s say Thole hits .318, has a .355 OBP and throws out 24% of opposing baserunners. Would you find that acceptable from a catcher? Well, that’s what Paul Lo Duca did in 2006 for the Mets and he made the All-Star team. We saw Thole match those numbers last year in Double-A (he threw out 30% of runners). In his brief time in the majors he hit .321 with a .356 OBP and threw out 33% of runners who tried to steal.

Thole may not hit a HR in 500 ABs (Lo Duca hit a grand total of 5 in his 2006 All-Star season). Let’s say that Thole matches his .396 SLG in the majors last year over a full season of ABs. So, we have a .318/.355/.396 catcher who throws out 33% of his opposing baserunners. Just how bad does his defense have to be to negate that? I would say it would have to be much worse than Mike Piazza at first base, much worse than Castillo at second base, much worse than Shawn Green in right field.

But because rumors of his bad defense far exceed the actual results, the Mets are going to give up 70 points of OBP in the catching spot this season. In 11 years in the majors, Rod Barajas has a .284 OBP. He had a .258 OBP last year, which was the 12th-worst mark of anyone in the majors the last 20 years who had 400 or more PAs. And it’s not like Barajas makes it up in SLG. His .403 mark was hardly better than what Thole did.

The Mets once played Mackey Sasser behind the plate, and he couldn’t even throw the ball back to the pitcher. How bad does Thole’s defense have to be to compete with that? So, before you downgrade Thole because he’s “weak” on defense, take a broader look at the subject. Yes, he gives up some passed balls. Well Bengie Molina gave up 16 passed balls in 2007 but that didn’t stop the Mets from thinking he would be a good defensive catcher.

And the kicker is that Barajas is going to stink up the joint and the Mets are going to call Thole up in the middle of the year. And Thole’s defense is going to be acceptable and his offense is going to be pretty good and people are going to say with a straight face that 75 games of “seasoning” at Triple-A is what turned his defense around.

5. Jon Niese, LHP, International League/Majors, 5-6, 3.82 ERA, 82 Ks in 94.1 IP

Niese got off to a horrible start last year in Buffalo. But in his last eight starts he was 5-1 with a 0.96 ERA with 46 Ks and 13 BB in 56.1 IP. Niese is not overpowering but he throws hard enough (89.5) for a lefty with his type of big curveball. With his lack of dominating stuff, he needs good command to succeed in the majors. In 23 games at Triple-A over parts of two seasons, Niese had a 2.7 BB/9 so he is certainly capable of that. Right now the big concern is how well he returns from last year’s gruesome hamstring injury. Early results are encouraging and he’s a much better candidate for the 5th SP job than Fernando Nieve.

4. Ike Davis, 1B, Florida State League/Eastern League, .309/.386/.565

When showing the numbers for a person who played with multiple teams, I normally pick the squad he played more with and use that one. But for Davis, the above line is from Double-A, because it was so impressive and was very close in PA (255-233) with what he had in Single-A. Davis followed that up with a .341/.394/.565 line in the Arizona Fall League. There is an awful lot to like about Davis but he is not ready for a job in the majors yet. He had a .381 BABIP in the Eastern League last year and he struck out 29% of the time. The MLE calculator at translates his fine hitting at Double-A to a .233/.294/.403 line in the majors. But he made tremendous progress last season and could certainly become an above-average first baseman, he is supposed to be a good fielder, if everything breaks right.

3. Wilmer Flores, SS, South Atlantic League, .264/.305/.332

Those are some ugly numbers, especially for a guy ranked this high. But they were put up in a full-season league by a 17-year old. Expectations for Flores were through the roof after his .310/.352/.490 in the rookie-level Appalachian League in 2008. He really needs to repeat this level or at least start out the season back in the Sally. This time last year he was being compared to Miguel Cabrera. Not many people are still making that comparison, although it remains his upside. It’s way too soon to panic or give up on Flores. Davis, who had three seasons of college ball under his belt, hit .256/.326/.326 in rookie ball in 2008 and turned it around last year. No one should be surprised when Flores does that in 2010.

2. Jenrry Mejia, RHP, Florida State League/Eastern League, 4-1, 1.97 ERA, 44 Ks in 50.1 IP

This is the player who most consider to be the Mets’ top prospect. Mejia has electric stuff but he was roughed up in both Double-A and the Arizona Fall League last year. There’s talk about having Mejia open the season in the bullpen for New York but that would be a mistake. True, it’s not a bad place to break in a young starter, but Mejia needs innings and it would be nice to see at least one win in Double-A on his resume before he joins the Mets.

1. Fernando Martinez, OF, International League/Majors, .290/.337/.540

For years, Martinez has rated as the club’s top prospect due to his tools and his age. Then last year he finally has some performance to match his reputation and most analysts drop him beneath Mejia. Martinez hit for power and he hit for average. He hit well both at home and on the road. Martinez K/% was just 18.8 percent. But he did poorly in a brief stint with the Mets and got hurt again. Certainly it is alarming the number of times he has been injured and I do believe that there is at least some skill to remaining healthy. But anybody who posts a .250 ISO in Triple-A as a 20-year old is someone special.

Honorable Mention/Names to Remember

Brad Holt, Jeurys Familia, Kyle Allen, Juan Urbina, Steve Matz, Zach Dotson, Jefry Marte, Tobi Stoner.

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