Wow, Marfig!
I'll start this off with a statement that may stop anyone from reading the rest of my opinion: I have not played, nor do I care to play Mass Effect - 1, 2, or 3. But I have read a lot of the story and the game choices, as well as the critiques by both players and reviewers.
I'm left with a weird feeling somewhat like Marfig: the story got too big, too self-referential, and nobody said "wait, what?!" Bioware has had a history of this for a while now, and fans have not helped clip its wings back to a story that could continue to suspend disbelief.
That being said, maybe I'm missing something but I kind of feel like fans are also being a bit crappy. There are stories that are tragedies - and what is a game but an interactive story? Not every game should be a happy ending. Not every movie gives us a ray of hope (ever see Requiem for a Dream? Read Romeo and Juliet or Othello? Or any Michael Crichton novel?!)
Bioware created a story that has gripped you sufficiently that you have spent $180 and taken a personal interest and ownership in the well-being of your character and the world that you have saved. Where is the failure in that?! You (general, not you personally, Doomsday) the player didn't create the story, you participated as an observer and were given the illusion of control while a story unwound around you. To me, this is perfection of the theatrical "fourth wall" - a world so believable that you took ownership of it and your seeming impact on it.
Though my understanding of the ending in context of the game universe does make it feel out of place, the biggest complaint everyone has isn't that the lead-up to your decision is completely silly (which it is), it's that there's no real HAPPY ending that stems from the final decision. That all the fighting and survival and struggle end up with someone gettin' screwed bigtime.
And in truth, that's kind of how war goes. Sometimes Private Ryan doesn't get saved, sometimes winning the war involves blasting your own and every other involved party's land into bloody trenches and all that you get at the end is left alone to rebuild.
All the talking and arguing over the unhappy ending, to me, validates it as a writer's decision: a story has been told, believable enough to make players care THIS MUCH that their own version of Sheperd be able to finally kick back and have a beer in a world s/he saved. Every story has to end - and sometimes that's just not the ending. If you're this angry about those being your choices, you should smile - the game did a great job connecting you just like an oscar-winning film or award-winning book. It may not be happy, but it's art.
That said, I'd personally be kinda mad about the 5 minutes leading UP to that choice...I mean, seriously...W. T. F. ??