the problem - as a really smart guy previously said - wasn't with ME3's ending, but with ME2's beginning.
The reason ME1 works so well, as a story, is because the Hero (tm) is Defiantly Facing (tm) some Insurmountable Odds (tm).
google it, i'm sure Tv Tropes has an article somewhere.
Explained in simple english, we know that Shepard cannot win. Humanity may be able to destroy 1 reaper in unusual conditions with combined effort, but they have no realistic chance of surviving the harvest. We love the fact that Shepard says "i'm gonna try to win to my last breath", because we love the Defiant Hero. Even though we know he can't win.
Which is why ME1 was so cool; it's the same kind of cool when the Black Guy (tm) in the zombie movie decides it's time to sacrifice himself, he grabs that belted M60 and faces off a horde of zombies while the white guy hero and the blond girl escape.
YOU KNOW HE'S GON' DIE, but he's sooooo cool.
And then in ME2 they chickened out of this narrative and what-if-shepard-wins, because of course they did.
So, removing the negatives, you remove the positives as well. Removing the "reapers equals certain death" you remove the key element of fascination with the story, which is " what if a Hero faces an enemy who cannot be beaten?". It's another facet of the tragic hero, not too different than Batman, or Doctor Manhattan, or even frikin' Superman in some of his stories, the hero who keep's on 'heroing despite being powerless to help/save/change Thing He Really Loves(tm).
mass effect was cool because for once, the good guys were gonna lose. this enemy is so stronk, the hero simply has no way to shape the story in a way that will make him win, and THAT was what was cool about it.
If i really had to milk it, because i owned Bioware or whatnot, i would have made a final scene where a whole bunch of reapers attack, and the join forces of humanity fight a desperate battle, but finally manage to kill off most of them ..
and then a HUGE force of reapers comes out of hyperspace. and that's it. game over.