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Well BA did their annual minor league organization rankings and the Yanks were one of the elite and the Mets were where no team ever wants to be. Yanks came in all the way at 5, Mets at 28.

5. New York Yankees
Cumulative Ranking, Last Five Years: No. 13
State Of The System: The Yankees continued their commitment to development in 2007, spending more money on the draft ($8.04 million) than any other club, remaining aggressive in Latin America (spending $1.1 million on Dominican outfielder Kevin DeLeon) and declining to ante up in a trade for Johan Santana. The strength of the system is pitching, and the best arms are all being counted on in New York (Joba Chamberlain, Ian Kennedy) or at least expected to contribute (Alan Horne, Jeff Marquez, Ross Ohlendorf) this season. OF Austin Jackson and Jose Tabata are further away but are clearly the top two position players in a system still building depth in that regard.
Best-Stocked Position: Righthanded starters. Chamberlain may have taken the American League by storm as a reliever, but he's a No. 1 starter in the making. Kennedy doesn't have the same kind of stuff, but he has an uncanny feel for pitching. Horne and Marquez are waiting in the wings, and Andrew Brackman and Dellin Betances have huge ceilings if they can regain full health.
Prepare For Takeoff: RHP Mark Melancon. One of several Yankees pitching prospects on the mend after Tommy John surgery, he has pitched just eight innings since signing for $600,000 in 2006. But he's finally 100 percent again and he has the stuff and makeup to once day succeed Mariano Rivera as New York's closer.
At A Crossroads: 3B Marcos Vechionacci. Long regarded as one of the system's best position prospects, he has seen his bat and power stall for three straight years in Class A. He's still just 21 and a strong athlete, but he needs to deliver on his promise."

"28. New York Mets
Cumulative Ranking, Last Five Years: No. 20
State Of The System: The Mets have been aggressive with international players such as OF Fernando Martinez and RHP Deolis Guerra, both in terms of spending to sign them and then pushing them through the system. At the same time, they've been conservative in the draft since giving Mike Pelfrey a $5.25 million major league contract in 2005. New York emptied its farm system by trading Guerra, OF Carlos Gomez and RHPs Kevin Mulvey and Philip Humber for Johan Santana, but the move was a no-brainer.
Best-Stocked Position: Righthanded relievers. The Santana trade left Eddie Kunz and Brant Rustich, both 2007 draft picks, as the system's best prospects behind Martinez. Rustich will give starting a try this year, while Kunz could be on the express route to Shea Stadium that Joe Smith took last year. Steven Clyne, the third college reliever the Mets drafted in the first three rounds last June, also could move quickly. Nick Carr is a starter for now but profiles better as a late-inning weapon out of the bullpen. Major league Rule 5 draft pick Steven Register has been impressive this spring.
Prepare For Takeoff: 3B Danny Murphy. In his first full pro season, he went to high Class A and ranked second in the Florida State League with 143 hits, then followed up with a strong performance in Hawaii Winter Baseball. He projects to hit for power as well, though he'll eventually have to move off the hot corner with David Wright in New York.
At A Crossroads: 1B Mike Carp. The Mets are worried about Carlos Delgado's hip, but there has been no talk of using Carp as a replacement if Delgado goes down. Carp needs to bounce back from a disastrous 2007, when he broke his right ring finger on an errant slide in big league camp and hit just .251 with 11 homers in Double-A once he returned. He also struggled against lefthanders and with his defense."

Well who didn't see that coming. You can clearly see why they have a huge difference between them when looking at signing bonuses. The most the Mets spent on any player last year was$720,000 and wouldn't pay up for talents like Brandon Efferson, while the Yankees spent OVER $720,000 3 times and gave their 1st round pick Andrew Backman $3,350,000 knowing he would need TJS. The Mets can make themselves an elite minor league organization if they use their 18th, 22nd, and 33rd picks wisely. Not to mention some of the high school talent that falls into much later rounds. But hey the Mets did used their prospects the exact way they are supposed to be used, by getting the top pitcher in all of baseball for 4 who no one knows how they will look in the future.

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