Baseball America ranks the Pirates' minor league system 16th among major league clubs, according to the Post-Gazette. As you probably already saw, Keith Law ranked the Pirates 18th. There are a couple mitigating factors here, such as that the Pirates also have a bunch of young and young-ish talent already in the majors, and that most of their minor league prospects were acquired in the last two drafts. I don't know anything about BA's methodology, but prospect lists of all stripes tend to rate players in AA and AAA most highly, which makes sense given the uncertainty in predicting the futures of minor leaguers, and it typically takes players a couple years to get to those levels. The Bucs' ranking could look much better next year depending on the fortunes of their zillions of low-minors arms (Quinton Miller, Zack Von Rosenberg, Colton Cain, Brett Lorin, Victor Black, Brooks Pounders, Zackry Dodson, Nate Baker, Justin Wilson, Trent Stevenson, etc.).
I don't think BA's ranking reflects poorly on the front office, despite the Pirates' strong emphasis on young players the past couple years. Rather, it shows that there is still work to be done, and that it takes a while to clean up a mess as big as the one Dave Littlefield left. (The Bucs' farm system was ranked 26th in 2008, shortly after Littlefield departed.) A look at Altoona's 2009 roster is instructive--yes, Neal Huntington acquisitions like Pedro Alvarez, Jose Tabata, Tim Alderson and Gorkys Hernandez did play, but Alvarez was the only Huntington draftee to get there. It takes a while for most players to get from the draft to Class AA, and that's when the minor leagues' chattering class really starts paying attention. Most of the rest of Altoona's players were disappointing or semi-disappointing Littlefield acquisitions (like Danny Moskos, Jason Delaney, Brian Friday, Jamie Romak, Steve Lerud, Shelby Ford, Jared Hughes, James Boone, Jim Negrych and Brad Corley) or pure organizational guys. The only legitimate Littlefield prospect who played there was Brad Lincoln. That's what happens when you have drafts like this.
The new front office has done very well with its first two drafts, but as the BA ranking shows, the Pirates' system is still middle-of-the-pack. It will probably be higher next year, but the Pirates can't waver. They need more great drafts and some big-bonus international signings--of which there have been none reported so far this year--to keep climbing uphill.