I don't remember whether it was this board or elsewhere that the current process of pitcher conditioning (and what I call "babying" pitchers' arms) was discussed recently. At any rate, one side believes that strict adherance to pitch counts and inning counts is a must..... while others believe that such restrictions can be overprotective and can prevent pitchers from developing the arm strength they need. (While I believe there's a place for pitch counts, I tend to fall into the latter camp.)
The article linked below is one of the best I've read in recent times. There's much of interest throughout the article..... but you'll find several references in the body which suggest that the Pirates have been among the "worst "offenders, not only in terms of "over-emphasizing" strict pitch counts, but also in not allowing long toss. In fact, this may be the reason that we've seen so many Pirate pitching prospects LOSE velocity.
In my opinion, regardless of which side of the argument you're on, the article is a good read and provides a lot of food for thought on the subject.