Here's Baseball America's Top 10 Prospects list for the Pirates. There's nothing very surprising and nothing too critical of the Pirates' management, which is too bad - any team that has Jose Bautista as its #5 prospect needs to get its farm system in order.
Depending on who was eligible, the only major change I'd make is to add Ronny Paulino and subtract Bryan Bullington. Outside of his draft position, there's no reason to think Bullington is a good prospect at this point. He's not young, his bounce-back season this year wasn't even all that good, and he's out until at least June.