What I agree with most in your post is the bench problems. In the WS year we had guys like Willie Harris, Geoff Blum, Chris Widger and of course TIMO. While that dosent seem like much, they all knew their roles and were very productive when called upon.
Our bench has stunk for a few years now, and the insistance of using 12-13 pitchers on the roster limits the guys we have on the bench.
I am not sure if this equates to guys tiring out and needing rest that the bench players can provide or not, but what I do know is that all great teams have productive bench players for whatever role needed.