The Hardball Times, one of the best baseball information sites out there, put out a piece ranking all 30 minor league systems in baseball. The Phillies system ends up at #10 overall, namely on the strength of our pitching, which was ranked 4th overall. Here is an excerpt, but be sure and check the link above for the full piece.
To keep things simple, I used a single stat for every pitcher and hitter in the minors. OPS was a natural choice for hitters, and to keep the graphs (which we’ll get to a bit later) on the same scale, I used OPS against for pitchers. To enable comparisons of everyone from Low-A to Triple-A on the same scale, I used equivalent (MLE) OPS, which is adjusted for park, league and level.
I took into account only two other variables for each player: their playing time and their age. It’s foolish to compare a 21-year-old in the Florida State League to a 25-year-old in the International League, and, as you’ll see in a moment, my ranking approach reflects that.
I considered playing time mainly to differentiate relief pitchers from starters. A team with a bunch of great relief prospects doesn’t have as strong a system as a team with several good starting prospects. (You could argue that adjusting for playing time isn’t sufficient, especially since differences in OPS against will be more extreme for relievers.)
First, I found averages and distributions for every age throughout the minors. In other words, I could compare every player to the average production from his age group. I included all players with reasonable playing time between the ages of 19 and 27—younger than 19, there are only a few players at low-A or above in all of baseball, and older than 27, players don’t really count as prospects anymore. (You could set the age limit lower, of course. It doesn’t end up mattering very much.)
Then, for every player in the minors, I determined whether he was above average for his age group, and whether he was in the 90th percentile or higher for his age group. (I also determined whether he was in the 75th percentile or higher, which helps make the graphs more interesting, but doesn’t affect the rankings.)