What that means for rankings of team's minor league systems is that even the difference between ranking first and last may not hold up when you look back on the careers of the players in the systems. Most systems will have less than 10 players in them at any one time who will make significant future contributions at the major league levels. By significant, I mean players who are regular starters or play a major role in the bullpen. So just a couple of players doing better or worse than expected can switch the rankings of two teams around.
For an example, lets look at the players who have significant major league experience and were prospects in the Twins minor league system ten years ago, after the 2011 season:
Ranking them on their major league contributions these six have had significant major league roles:
For contrast, here is Baseball America's top ten for that year:
1) Joe Mauer
2) Justin Morneau
3) Michael Cuddyer
4) Michael Restovich
5) Adam Johnson
6) Brad Thomas
7) Juan Rincon
8) Rob Bowen
9) Matt Kinney
So, as people try to evaluate how the strength of the Twins minor league system, take any conclusions with a grain of salt. We all hope guys like Sano and Hick will become great players like Mauer and Morneau. But its just as likely some guy we haven't heard of will turn into Jason Kubel.