Sam Miller at Baseball Prospectus has a great article comparing the best and worst farm systems in 2004. Technically the Astros were in 29th but the Expos were in a "weird place" so he decided to do the Astros instead. He looks year by year of what each system (Brewers were #1 at the time) got out of their top 30 prospects. Since it is "premium content" I won't post much but here are a few nuggets:
In 2012, the Astros don’t get a single at-bat or inning from a member of the 2004 prospect group, or from any player acquired directly or indirectly for a member of the 2004 prospect group....The Brewers still have Rickie Weeks and Corey Hart signed, Carlos Gomez (in return for J.J. Hardy) signed, and two draft picks that produced legit prospects in the current system. Which means they could actually still get more value out of their 2004 farm system from 2013 on than the Astros got in total.
The Astros still have two players in their farm system who were supplemental picks of players who were lost to free agency in this group: Mike Kvasnicka and Mike Foltynewicz.
Combined WARP of the 2004 prospects for the Astros (+ players acquired through them) 12.4..... For the Brewers... 74.9
And that is how we got into this mess. It didn't happen overnight and it isn't going away overnight.