People tend to feel very strongly about Mets prospects for some reason. And it doesn't seem to be exclusive to Mets fans. If you ask someone who follows baseball and prospects what they think of the Mets minor league system, they will almost always tell you one of two things:
Mets prospects are overrated.
Mets system is underrated.
Cognitive dissonance, I know, is setting in. How could those BOTH be true? Well... my observations have led me to discover Mets Prospect-itis. Here are the symptoms:
First, typically, one or maybe two of the Mets high-ceiling prospects will become grossly overrated. I am looking at you, Alex Escobar, Paul Wilson, Jason Isringhausen, and Gregg Jeffries. Then, everyone else in the system, for some reason, gets disregarded as useless and will amount to nothing. This is Heath Bell, Ty Wigginton, and a multitude of others.
To demonstrate this, I'm going to pick a Mets prospect that I like and compare him to someone in another system who I believe is pretty similar. Neither have 98 mph fastballs, have destroyed the minor leagues, or are surrounded by a ton of hype. Here are how the two have been described by one of my favorites, John Sickels:
Prospect X, Grade A-: I love this guy. If [other prospect on list] could become Oswalt, [he] could become John Lackey.
Prospect Z, Grade B: Assuming the hamstring is OK, I see him as a slightly above average starting pitcher, classic number three guy.
So Prospect X he sees as a fringe ace, while Prospect Z he sees as a middling, do-nothing-but-be-kinda-decent starter. They must be miles apart according to their minor league track records or physical ability, right? Wrong.
So now, let's compare the two prospects and what they did in each year of their career thus far:
Age 20: Both prospects fare well, with Prospect Z a whole level higher than Prospect X.
Prospect X - A: 3.02 ERA, 1.29 WHIP, 10.2 k/9
Prospect Z - A+: 4.19 ERA, 1.35 WHIP, 7.4 k/9
Age 21: Prospect X dominated A+ ball and then moved up to AA, where he did very well. Prospect Z, who is obviously a Met because he's being rushed, did well in AA and then replicated that performance in AAA.
Prospect X - A+: 1.84 ERA, 0.96 WHIP, 10.1 k/9
Prospect X - AA: 3.15 ERA, 1.30 WHIP, 9.1 k/9
Prospect Z - AA: 3.04 ERA, 1.30 WHIP, 8.1 k/9
Prospect Z - AAA: 3.40 ERA, 1.21 WHIP, 7.3 k/9
Age 22: Prospect X again elevated his game, pitching great in AAA after a promotion. Prospect Z pitched in AAA successfully again, and then did quite well in the majors for a young guy breaking in for the first time.
X - AA: 3.85 ERA, 1.36 WHIP, 6.8 k/9
X - AAA: 2.72 ERA, 1.19 WHIP, 9.3 k/9
Z - AAA: 3.82 ERA, 1.28 WHIP, 7.8 k/9
Z - MLB: 4.21 ERA, 1.40 WHIP, 6.3 k/9
Age 23: Prospect X continued his steady ascent - a slight step back in AAA, but then held his own in the majors. Prospect Z is 23 this year.
2009 - AAA - 23: 3.40 ERA, 1.25 WHIP, 7.9 k/9
2009 - MLB - 23: 3.72 ERA, 1.27 WHIP, 8.9 k/9
So why? All along, Prospect Z was about a year ahead of Prospect X. It might be that Prospect X has better "stuff" or something else - but you'd have to make a serious argument based on that in order to project him TWO grades higher than the other guy.
Prospect X is Wade Davis, a fine prospect. I think Wade Davis is going to be very good. He's 6'5", 220 lbs. He throws a 92 mph fastball about 3/4 of the time, with a curveball his second most common offering at 12.6% and a slider at 8.6%. The fastball and curveball grade out as significantly above average, while the slider is average.
Prospect Z is the Mets' own Jon Niese. Niese is listed as 6'3", 190 lbs. He throws a fastball which averages 89.6 mph about 60% of the time, and mixes in a cutter and curveball each about 16% of the time. Both of those pitches grade as significantly above average as per Fangraphs.
This is obviously just one example out of a million-billion that are out there, but I think it's a strange bias that exists when it comes to our minor league system.
I am not arguing that Wade Davis is not a better prospect than Jon Niese. For what it's worth, I think he might be a hair better. But whether you prefer the stud right-hander who throws 92 with a great curveball or whether you prefer the left-hander who is younger and and has two plus off-speed pitches is a matter of taste. I don't see how it makes sense to call one Lackey and the other Jeff Suppan.
Any other examples of this that you can think of?
 No, I am not willing to include Lastings Milledge in this group. Stop asking.
 Some recent former Mets farmhands who never received mainsteam hype who are useful major leaguers? Jesus Flores, Matt Lindstrom, Brian Bannister, Yusmeiro Petit, Carlos Gomez, Angel Pagan.
 I'm not a prospect maven, but there are a couple other rankings around the league that have baffled me. Maybe we can get John Sickels in here and ask him how he values Niese against some other pitchers who he had graded ahead of him, like Tanner Scheppers of the Rangers, or Jacob Turner of the Tigers.
Amazin Avenue relays a chart which was drawn up which graphically displays all the prospect rankings made by Sickels. For what it is worth, Sickels only gave eight pitching prospects in the entire game an A- or better. 18 got a B+ and 32 got a B, like Niese.
Depending on where they landed on each letter, Sickels believes that Wade Davis is between the 4th to 8th best pitching prospect in the game, but Niese is only the 27th to 58th best. I realize these rankings are preliminary and unscientific, but that's quite the discrepancy.
 And this opinion does take into account the fact that Niese hurt his hamstring last year. That is an injury unrelated to his elbow/shoulder area and he didn't pitch on it while injured. He ought to be fine. Even if this stunted his development somewhat, he is still 13 months younger than Davis and is still in the same neighborhood as a prospect.