Sure, it's nice to have baseball's best farm system -- but the truth is that it's still one degree removed from the thing you actually want. Baseball franchises want to win games -- and if you aren't a winning team, at least a good farm system is a nice consolation.
Some teams near the bottom of these farm system rankings are there because they're either winning all the time (often subtracting prospects as often as they're adding them) or have recently graduated a bunch of good young core players and are waiting on the next wave(s).