Fernando Martinez or Wilmer Flores – which one got top billing?  Read on to see my list of the team’s top 10 prospects.

Last year after the Johan Santana trade, many people were complaining about how thin the Mets’ farm system was.  But then 2008 came and the team got strong contributions from Daniel Murphy and Nick Evans along with contributing efforts from several different pitchers who retained their rookie status.  Suddenly the system doesn’t look barren at all.  While there is certainly a dropoff after the top three, there are several players who did not make the list – most notably 2008 picks Ike Davis and Reese Havens – who could contribute to a pennant contender.

So, here’s how I view the Mets system.

10. Josh Thole, catcher, Florida State League, .300/.382/.427

Fernando Pena is frequently trotted out as the top catching prospect on the team, but he has yet to hit in two stints in the Low-A South Atlantic League.  Thole meanwhile put up a nice line in the pitcher-friendly FSL.  Thole’s .427 slugging may not seem like much, but David Wright posted a .459 mark while in the same league and park.  And that average and on-base percentage should not be dismissed.  The big key with Thole will be if he can handle the position defensively.  A catcher in high school, the Mets moved him to first base before putting him back behind the dish last year.  His defense will be a work in progress as he advances through the system.

9. Nick Evans, outfield/first base, Eastern League, .311/.365/.561

He was part of an effective platoon in left field in September with Daniel Murphy (who is not eligible for this list) but as the righty part, he got far fewer at-bats.  Evans did very well versus southpaws in the majors but looked completely overmatched versus righties.  His power definitely makes him intriguing and if he can repeat his 2008 numbers, whether at Triple-A or the majors, he could earn a shot as the club’s first baseman once Delgado moves on or retires.

8. Bobby Parnell, RHP, Eastern/ International League, 10-6, 4.30, 91 Ks, 127.2 IP

Parnell’s stuff far outstrips his production up until this point of his career.  But the Mets constantly talk about him as one of their top prospects and that just can’t be ignored.  Parnell’s line listed above was as a starting pitcher in Double-A.  He was 2-2 with a 6.64 ERA in five games at Triple-A and he also made six appearances with the Mets.  Parnell basically is a two-pitch pitcher and will probably end up in the bullpen permanently.  But his fastball is in the mid-90s and an arm like that is something to keep tabs on.

7. Dillon Gee, RHP, FSL/Eastern, 8-6, 3.25, 94 Ks, 127.1 IP

A 21st-round draft pick in 2007, Gee is not overpowering but has at least an average fastball with good movement.  He has excellent control which led to a combined 114:24 strikeout:walk ratio last year.  The numbers above were in the FSL and Gee went 2-0 in four starts in Double-A, where he allowed just four ER in 27 IP.  He’s also pitching well in Winter Ball, where he is 4-0 with a 2.27 ERA in 10 games for Ponce in the Puerto Rican League.  Gee does not have star potential, but he could be a very effective #4 type starting pitcher.

6. Jenrry Mejia, RHP, Gulf Coast/New York-Penn League, 3-2, 3.49, 52 Ks, 56.2 IP

While Gee is further advanced, and more likely to remain a starting pitcher, Mejia gets the nod because you just can’t beat a fastball that hits 98 mph.  He will be 19 this coming baseball season and it’s possible he will pitch in the FSL, as the Mets like to be aggressive with their prospects.  Mejia has a good changeup and also features a curve.  The hope is he can stay in the rotation, but worst-case scenario is he becomes a flame-throwing relief pitcher, possibly a closer.

5. Brad Holt, RHP, NYP League, 5-3, 1.87, 96 K’s, 72.1 IP

A supplemental first-round pick for the loss of free agent Tom Glavine, Holt could not be more different from the soft-tossing lefty.  He consistently throws in the mid-90s, although the concern is the fastball is his only MLB-quality pitch.  The Mets want him to remain a starter and they compare him to Mike Pelfrey.

4. Jefry Marte, third base, Gulf Coast League, .325/.398/.532

While Wilmer Flores received most of the attention last year, Marte did equally well, although at a lower level.  The Mets rave about his bat speed, which is one of the best things you can hear about a young hitter.  Marte has an impact bat but the question is where he will end up on the field.  He’s a third baseman now but is unlikely to stay at the position.  The good news is the bat looks like it will play anywhere.  Given how the Mets like to push their top prospects, Marte will likely start the year in the full-season South Atlantic League.

3. Jon Niese, LHP, Eastern/International, 6-7, 3.04, 112 Ks, 124.1 IP

It looks like Niese will open the season as the team’s fifth starter.  I am a big fan and I think he’s got the potential to be a #2 type SP but I really think he needs some more time in the minors.  The above numbers are from Double-A and he has just seven Triple-A games under his belt.  Niese features a big curve and a fastball that reaches the low-90s, plenty of stuff for a lefty to succeed if he can throw strikes.

2. Fernando Martinez, outfield, Eastern League, .287/.340/.432

Injuries have slowed the development of Martinez, who was heralded as one of the top prospects in the game immediately after he was signed as a 16-year old.  Because of the injuries and the Mets aggressive approach with their young prospects, Martinez has yet to dominate a level in the minors.  But those numbers above were put up by a 19-year old in Double-A.  Some worry about if his power will develop but I think a full season at one level will give us a better indication of his HR capabilities.  Hopefully Martinez will get that this year in Triple-A.

1. Wilmer Flores, shortstop, Appalachian League/NYP, .310/.352/.490

Flores came onto the scene with a bang last year as a 16-year old in the APPY, where he posted the above numbers.  He turned 17 during the season and ended as the youngest player ever for the Mets’ Brooklyn affiliate in the New York-Penn league.  Flores even got a few games in at the South Atlantic League.  Like Marte, he’s got great bat speed and showed he could hit for both average and power.  He’s not as fast as Marte but is a better defender.  His arm strength was so good that there were debates about him being a pitcher.  However, at already 6-3, 175 pounds as a teenager, he will probably outgrow shortstop.  But this is a special player and the comparisons to Miguel Cabrera have already started.


Many argue about who should be the Mets top prospect – Flores or Martinez.  Martinez supporters will argue that Flores is where Martinez was in 2006 and that he should be first due to knocking at the door of the majors.  But I ultimately chose Flores because of the dual concerns surrounding injury and power production, the fact that Flores could stick in the infield and the belief that his upside is simply greater than that of Martinez.

The Mets have a nice collection of hitters and pitchers, although some may worry about the lack of upper level prospects.  But if Martinez and Niese can join Daniel Murphy as productive members of the team over the next two years, that will be excellent production from the farm system to complement the David Wright-Jose Reyes-Carlos Beltran-Johan Santana core and give the youngsters like Flores, Marte and Mejia time to develop.