Here is the problem in my opinion.
1) Chase for Velocity, this has really gone crazy in the last 10 year. A control pitcher people wouldn't give a look at. Look at how nobody mentions butto as a prospect the guy hit 92-93 occasionally rears back and hit 95. But 95 used to be impressive now 95 is like 91-92 10-15 years ago. Hence the mets wanted to see Megill over him, after seeing him fail and fail again. I don't think guys who throw low 90's even get scouted well, thing is if you have good off speed pitches and you have control, that is far more important than velocity an you have no clue where it is going, you see this a ton with relievers, they hit a ton of batter, simply nobody has a clue where the ball will end up.
I remember when degromm broke in. In the first couple of years he was a very good pitcher, and very few injuries, he threw 95-96 coming in. Inexplicably as his career went on he started to throw harder, heck he would often hit 100-102. Of course he went from a very good pitcher to possibly the best pitcher in baseball for several years. Problem is he became much less durable ultimately leading to arm troubles because in my opinion his career would of been different if he stood at 95-96, I believe he would of been more durable, not that we can ever prove that.
Look at the long career Justin Verlander had. He would often since at like 94-95, and only throw 97-99 in his prime when he needed to in big spots. That is pitching, that will help you with durability, hence the chase for velocity and trying to throw max velocity every pitch I think is creating a decent amount of problems.
2) The Clock- This has added to the pitching problems. If you give pitcher less time to rest in between pitches and they feel the need to rush to get the ball off. Your gonna get more injuries. Now as a fan I like the clock, but I can see why pitchers wouldn't ike it.
3) Sticky Stuff- Lets not forget this. If you have people needing to hold onto the ball tighter, there is a great chance of doing something to the shoulder and elbow. I believe this is another huge issue, that baseball has used the last several years that has made injuries rise as well.
I personally would let the sticky stuff in some form come back. I think that would help a great deal. I also think they need to teach pitchers, specifally when your a non reliever. I think Pitchers especially ones with high velocity, would be better sitting at 90% of max velocity most of the times, and use max velocity in spots. All is just my opinion of course.
