In advance of the top 100 prospects list, I've ranked the 30 MLB teams' farm systems based solely on the players currently in the organization who have not yet lost their major league rookie eligibility. Thus, Brett Lawrie doesn't count for the Toronto Blue Jays, but Mike Trout does still count for the Los Angeles Angels.
Past production of players doesn't factor into this. It ain't where you're from; it's where you're at.
Without Anthony Rizzo, they no longer have a top-25 prospect in their system, but in terms of total future value of players likely to play significant roles in the big leagues, they're ahead of everyone else. Some of these players, especially from the 2011 draft, will develop into stars. But there are so many prospects here with high floors, players who would be top-10 or top-five in other systems but are 11-20 here (such as Robbie Erlin or Edinson Rincon), that they are well-positioned to compete even with modest major league payrolls during the next five to six years. Fans who were upset at the sudden departures of GM Jed Hoyer and assistant GM Jason McLeod for the Cubs should find solace in the fact that the prospects they helped bring into the system (along with many other scouts and execs, including Chris Gwynn, now with Seattle, and Jaron Madison and Randy Smith, still in San Diego) remain in place.