I don't know if anyone else caught the MLB Network round table on this topic over the weekend but it was really interesting.
The general consensus was that the problem is starting in youth baseball. Year round teams and kids throwing off a mound are both problematic. Also too many kids throwing with fatigue.
ETA: Here's part of the show where they 
interviewed Dr. James Andrews.
		
 
		
	 
I watched it. I found it interesting that the ex-players like Kaat, House and Smoltz think pitchers don't throw 
enough to build up arm strength, whereas journalists and doctors think the opposite.
Kaat told an anecdote of when he and Tommy John were teammates with the White Sox in the early 70's, and the day after Kaat had thrown a nine inning game he was out throwing BP. John was shocked, as he only did running in between his starts. And Smoltz talked about how hard Leo Mazzone worked him, Maddux and Glavine in between starts.