The data on that stuff is mixed at best. Anecdotally people say the split is the worst pitch. Some studies say throwing hard makes injury more likely. some studies still think breaking balls are just as bad (high velocity definitely equals higher stress, but a curves at lower velocity may provide more stress than a straight pitch at the same velocity).
Clearly nobody knows anything about whether pitch counts and off-day throwing patterns really work.
The reality, IMO, is that there probably isn't any simple answer, that just like for most running backs in football it's inherently going to be a short career for most pitchers, but because baseball is not a contact sport it seems more dramatic. Like you say, it's not natural, but none of it is.
The Mets have this reputation but I think it's probably more about their media market and the high expectations (justifiably, at the moment). After all, four of the five Phillies starting pitchers from last season eventually went down right (didn't Eickhoff miss some time?).And Eflin and Thompson too. Two out of five already this year.
