I think Heilman's struggles, later revealed to be injury related, was the biggest hit to the pen even more than Wagner. If H was 100%, he would have been the closer at the end, and possibly have been able to go two innings at crunch time to keep the ball out of the hands of Ayala, Schoenweiss, Feliciano, et al.
I also think Manuel mixed and matched too much at the end. If you have a bunch of bad pitchers, and you pitch all of them every game, you're bound to be burned. You're better off sticking with the one guy who seems to be ok for more than 1 or 2 batters at a time. Then again, he didn't have much choice with Maine before the injury, Martinez, and Perez all being 6 inning guys even when they're good.
Ayala, Schoenweiss, Feliciano, et al... I think that's all that needs to be said when someone asks why the Mets bullpen wasn't very good.
In January of this year I said, "Wagner - ...His collapse towards the end of last year has me very nervous. I’m going to pass on Wagner this year, but he could be better than fine. You’ve been warned. Projections: 2-3/70/3.75/1.35/25 saves and Heilman takes over in August and gets 15 saves."
As you can see, Wagner's collapse was foreseeable. I think the Mets should've preemptively fixed the problem.