SOTD, I'm not a statistician by any means, because I'm terrible with creating formulas and the like. For example, Jackal's adjusted ERA crap confused the living hell out of me.
Anyway, let me say for one thing, that AAA leagues may not be the best place to look. Top prospects rarely spend that much time in AAA...a year is the maximum and that doesn't happen all that often as long as they fare well. It's seen as a place for players past their prime and others who'll never be solid regulars. Too many players with good stats will never become major leaguers. Some are 30. It's basically only a league to polish players up.
When looking at stats in lower levels, take this into consideration:
To judge a good hitter, look at K/BB. Good plate discipline is a must. High average...high OBP...look for a high amount of DOUBLES. Home runs don't always have to be there. Note that many players that are fresh out of High School have yet to fill out and thus don't have that much power. Those doubles will eventually turn into homers. A good example of this happening is Hermida. Always a good hitter...added the power.
At higher levels, looking at the HR total becomes more important. However, different players mature at different levels, so the age that one player develops power may be drastically different from another's.
For college players, you're going to want guys who are moving relatively fast, have a high average. Their power numbers should generally be much better, since they're older and have faced better competition in their lives.
About speed...make sure that the SB/CS is decent (but not for raw players) and that he's stealing a fair amount of bases. However, speed is best read about...so you must again, read here. For example, a guy like Hermida (same example) has been fairly decent on the basepaths stealing quite a few bases, but scouts say this is more due to a good understanding of baserunning and the lower level of competition. Due to his lack of great speed, he won't be able to do that as much at higher levels. Prince Fielder has also been surprisingly fast, but we all know that's probably not going to continue. And then there are unrefined speed demons that haven't figured out how to truly steal a bag. These players are great sleeper picks, because if they learn how to steal bases, they'll be superb. So again, you must read scouting reports to judge speed.
Pitchers are tough. They have a high injury risk. High School pitchers generally blitz through the lower levels okay. Then, they face troubles...like injuries, or tougher competition. Look for a good K/BB rate...and that he's not giving up too much. WHIP is important, as well. However, most top prospect pitchers seem to have great stats. I would read a lot about pitchers, though, as effectiveness and ceiling cannot always be shown in stats. For example, some pitchers who are of the finesse/control mode could have great stats (especially ones from college who are more developed), but they will not project as well as power pitchers who will be able to continue to dominate at higher levels.
Let me repeat the caveat: Early on in Minor League careers, the college players WILL be more advanced in stats and ETA than the HS kids.
Stats are only stats. They only take you so far. READ, READ, and READ more about prospects. There are certain facets of players, like certain tools and athleticism that may not always be sufficiently reflected just in stats.
The 20-80 scale is great to judge each individual tools. See what scouts say for each players' individual tools on the scale.
What I'm basically trying to say, is that I would not depend on stats much at all to judge talent. I would read scouting reports and see what they say about players. Of course, if your player ends up having a bad year and bad stats, then you have to take a step back and say...hmm...this may not be that good a player, or, he may take longer to develop.
I've never been a fervent supporter of the Moneyball/stats movement because there are so many intangibles in baseball, but this is even more true in the minor leagues, where the league is made, in terms of prospects, for developmental purposes. Development can be best read through reports. For example, if a playre was struggling with a bad batting average, you may just write him off. However, say a scout keys you in on the fact that he was adjusting his stance. You wouldn't have known that with pure stats.
I hope this helps a little, although it may not be exactly the answer you were looking for.