Forget innings pitched. Bauer averaged 129 pitches an outing. That's the concerning part. Even in the majors you start getting concerned about a starter at 80 pitches and generally try to keep them around 100 unless they are throwing a shutout or something. Bauer's number would be very high for any level and a MLB manager would take a lot of criticism for over-throwing him -- especially for a young arm.
Not everyone believes in pitch count/shoulder problems, but those who do like to point out what Lasorda did to every decent starter in the Dodgers organization, or what the Cubs did to Kerry Wood. I always think of Livan Hernandez throwing 9 complete games and 255 innings for Montreal in 2004, the last year; he forever lost pop on his fastball and started racking up injuries. Not that the Giants did him any favors before that. His pitch count regularly got into the 130s, and this is a guy that was built to be an innings eater with his bulk and strong legs.
Bauer is not 235 lbs with Roger Clemons thighs. He's 185 with a throwing motion that puts a lot of stress on his shoulder and elbow. He doesn't generate enough power from his legs and hips, so it's something he's going to have to work on in the minors. The other thing he could do is simply throw more strikes and work on getting easy outs to get his pitch count down. Just fixing his change up, which is weakest pitch and lacks real control, could go a long way to doing that.
