Spoilers follow
So my main problem with some of the endings is that I just can't make sense of them.
A synthesis between human and machines where everyone is suddenly converted to have little green lines all over them? My suspension of disbelief just can't go that far, it's too farfetched.
I also fail to understand why the Geth and EDI die in the ending where you destroy the reapers - they are in no way connected to the catalyst so how does it destroy them?
Maybe I'm missing something...