I'm replying on my phone so I can't do a single post with different reply quotes, but some more thoughts.  
What I saw in a couple responses was a desire for every last plot device to be wrapped up.  This runs contrary to what epic science fiction needs to be, for two reasons:
1.   It removes a lot of the mystery.  I think the TV show Lost was saddled with a somewhat unfortunate ending because the writers were trying to serve too many masters.  I would have liked it better if they'd ended that show and not attempted to answer every last damn thing that they didn't have a reasonable answer for.  
2.   For epic sci fi to maintain its sense of wonder, it needs to end on a somewhat nebulous note.  If the game ended with Shepherd and pals kicking back on the Normandy with a beer and some laughs, how lame would that be?  Nobody wants that shit.  
The game ended with the reapers recognizing that all organic life forms might have a shot at a future after all, Shepherd made the sacrifice that mattered, the Illusive Man made a Vader-esque redemption, and we know the fate of Shepherd's crew and the universe as a whole. 
I really have a hard time finding massive problems with this ending, and an even harder time understanding the level of sheer hate leveled at it.  I have to kick off for the night, but I'm looking forward to reading more of this thread tomorrow.