Stark had the following to say about the move:
"With all of the trades, drafted players, and international signs the last two years, we have limited opportunities for many talented players. Ultimately we have decided to give those innings to other pitchers. While Nelson had performed well at the lower levels, we must allocate innings based on what we think a pitcher is going to do rather than just what he has done. A left-handed pitcher with a changeup is going to have significant success against young hitters and that is what Nelson did."
Pereira, in case you don't recall, is a lefty pitcher who put himself on the map with some great numbers as a 19-year-old in rookie ball in 2008. The Pirates moved him up to State College in 2009, and he struck out more than a batter an inning as a 20-year-old. Normally, a lefty who can succeed at any level in the states at ages 19 and 20 is worth holding onto. However, Pereira struggled with his control, is an extreme flyball pitcher, and doesn't throw hard. Essentially, he's the archetype of the pitcher who can succeed in the low minors but not at the higher levels, where hitters have plate discipline and power. He's also exactly the kind of pitcher the Pirates under Huntington seem totally uninterested in--think of Todd Redmond, who's similar in many ways and who was sent to the Braves for Tyler Yates not long after Huntington arrived. WTM writes a bit here about some of the changes he's seeing in the low minors--now, their pitchers all throw hard.
Ultimately, releasing him is a judgment call that can be debated, and I'm not really sure why the Bucs didn't make him a reliever. But the fact that they were even in a position to jettison a player like this speaks volumes about the improved depth in the farm system. It would not surprise me if Pereira caught on with another team and pitched very well in Class A somewhere, thus sending Bucs fans into fits of rage, but the Pirates already have a ton of interesting pitchers at the Class A level, and for a player like Pereira, Class A performance probably won't translate well to good performance at the higher levels. I don't mean to frame this in an entirely positive way, but still--I don't think there's any way the Pirates could have released a player like this even a year ago.
UPDATE: The Post-Gazette confirms the Pereira release and has a bunch of others, some of which have already been reported elsewhere. Among them are Harrison Bishop (a vaguely interesting Class A+ reliever), Chris Garcia (a former Angels prospect who was acquired out of independent ball this winter), and Kyle Bloom (who looked like a prospect at one point and was a Rule 5 pick by the Tigers in the 2008-09 offseason).