Now that I've done the AtP for all of the positional players, I've got my Top 15 prospects list ready. I did it all on my own, but the list is really similar to many of the others out there, with minor variations.
First, I'll explain my methodology. I first made a system from 59 (complete non-prospect) to 100 (potential all-time great). The number assigned to each person takes two things into account: the upside, and the bust potential. For instance, I have 75 as a MLB backup, but Junior Lake is a 75. His upside is more like an 85, but his bust chance is way higher than normal, so I settled on 75. I then went down the minors and found 21 people that I thought were greater than 59. 6 missed the cut (Justin Marra, Rock Shoulders, Greg Rohan, Zeke DeVoss, Ronald Torreyes, Stephen Bruno, and Jae-Hoon Ha).
The grading system is as follows:
100 is a potential inner-circle HOF that has a very low chance to bust. Maybe .5 prospects a year would get this rating, and none would this year.
95 is a potential HOF that has a low to mid chance to bust. This is probably the top 4-6 prospects.
90 is a potential MVP candidate at some point. This is probably the top 20 or so prospects.
85 is a potential All-Star candidate at some point. This is probably the top 50-60 prospects.
80 is a potential MLB regular. From this point, it's hard to put a number on the total prospects, but consider that there are 750 major league players at one time.
75 is a likely MLB backup.
70 is a potential backup, or a player without high upside but with a relatively high floor.
65 is a potential backup with low upside but a potential low floor.
60 is a longshot MLB backup but with some skill that makes them interesting.
Without further ado, here's the list.
#1 (90) Javier Baez SS
Baez is young and has a relatively high chance to bust for someone as good a prospect as he is. He doesn't have the greatest patience and might not be a plus defender anywhere on the infield (though he's rapidly improving at short). That being said, he's got truly elite bat speed and good power. He's young, arrogant, and good. If he repeats his 2012 performance at A+/AA, he'll be in the majors next year at just 20 years old.
#2 (87) Albert Almora CF
Almora might not ever garner MVP votes, but for a youngster he has a seemingly high floor. He can play great defense at CF even now, and is so advanced for the leagues he was in last year that he almost never struck out. He is the most likely of the Big Three prospects to actually play meaningfully in the majors, albeit with the lowest upside.
#3 (85) Jorge Soler RF-CF
Soler has 70 power (on the 20-80) scale, which is rarer than it sounds. He might have the only 80 tool in the whole organization with his arm. (EDIT: This is more apt of Junior Lake. Soler does have a fantastic arm, but Lake's is better.) His batting eye needs a little work, but not much, and he can run enough to play CF (but hasn't, inexplicably). He's got a chance to bust out for sure, but the upside is there.
#4 (82) Dan Vogelbach 1B-DH
#4 (82) Brett Jackson CF-OF
Vogelbach and Jackson are tied at 4 in my list, though they are completely different prospects. Vogelbach is a huge bust risk with his body (and the quick changes that he's making to it). He could lose his power with his weight or eat himself out of the league. That being said, he's got great plate discipline and hurts balls real bad. He's a defensive liability but could be an incredible force in the lineup. Brett Jackson is the other way: he can play good defense at any outfield position, but is a threat to strike out 40% in the majors. He works counts and has okay-ish power, and at worst right now he's a passable 4thOF. If the new swing really works, he could play in a few All-Star games, and if it doesn't, he's still got the toolset of a backup.
#6 (80) Gioskar Amaya 2B
I'm a huge Amaya fan. His plate discipline has always been solid (9% walk rate), and his power has developed every year. It's not common for 2B to put up ISOs of .200, but Amaya did last year. He's got to work on fighting his strikeouts, but the combination of speed, power, and patience make Amaya a potential great at 2B in the (distant) future.
#7 (78) Arismendy Alcantara SS
Alcantara doesn't walk very much, but he also plays the more premium position (relative to Amaya). Alcantara is also a switch hitter, so if he can cultivate that skill he could be slightly more valuable. He was injured last year, but all signs point to him being 100% now. I'm banking on him picking up where he left off in 2012.
#8 (77) Jeimer Candelario 3B/LF
Candelario's biggest concern is his potential demotion to 1B from 3B. Candelario is young and he has good plate discipline for his age, but his drastically lower BABIP in '12 showed people what Candelario's true talent level was more like (and it was still high-ish at .327). Candelario is a guy who could really shoot up this board later on, but he's also equally likely to just be another dork at 1B/LF that busts out at AA.
#9 (75) Logan Watkins UTIL
#9 (75) Dave Sappelt OF
#9 (75) Marco Hernandez SS
#9 (75) Christian Villaneuva 3B
#9 (75) Junior Lake 3B
#9 (75) Matt Szczur CF-OF
75 is basically where prospects are too diverse to dissect meaningfully. Each of these guys are at different stages at their prospect-hood. I think Hernandez and Lake have the best chance to be above-average MLB starters, but they also have the best chance of busting out and never making it. Sappelt and Watkins are almost both shoo-ins to log some time at the Majors (Watkins have a better chance of starting at some point in a DeRosa role), but are unlikely to ever be more than primary backups. Villanueva and Szczur are somewhere in between those two groups. I can find something I like about each of these guys, and another thing I don't like about all of them. You could put these 6 guys in literally any order and I couldn't honestly disagree with you.
#15 (73) Josh Vitters 3B
Vitters still has a chance to make it, but boy was he awful in his first cup last year. His poor play in 3B was topped only by his ineptitude at the plate. He has a pretty swing and a history of making progress the longer he stays at a level, but he's only worth anything if he can stick at 3B and he can more than double his BABIP from last year (double it, his OBP "climbs" to a Barney-esque .308). It's hard to believe he's only going to be 23 next year, but he's had 2,227 professional plate appearances in his career. It's hard to imagine a great change in his skills now.