I don't think the choices themselves were bad. And the extended endings helped a little bit.
It was like you said, no epic battle (boss battles are fucking terribad, such an awful concept for a game like ME but...a fight with tons of enemies and a couple big ones would be cool), the "deus ex machina" aspect which I hated, and a couple other small issues I had.
I didn't loathe it, but I didn't like it. Could have been done way better and frankly it surprised me that Bioware told such a great story with such fantastic moments I'll never forget, but then ended it like that.
Anyways, the series is still one of the best ever. Like I said, some moments in those games I will NEVER forget. And to be honest as much as we rag on 3's ending, a lot of those moments took place in 3.