I have a weird opinion about the way the story turns out in 3.
The first 2 games have a lot of personal stories, and conflict between races, with the looming threat of the Reapers in the background.
Once 3 rolls around, the Reapers are on the offensive, and the puny organic races are scrambling to finish the only hope they have left to survive, the Crucible.
In the grand scheme of things, all of those personal stories and conflicts mean absolutely nothing, the Reapers are a civilization destroying "evil" force that cares nothing for the squabbles of the humans and Cerberus, or the tensions between the Humans and the Turians from the first contact war. Or the Krogan genophage.
It literally means nothing to them, and the fact that once you get to London, everything has turned to so much shit, and organics are on such the backfoot, that any inkling of the stuff you have done, or the conflicts between races, does not matter any more, because if this fails, its all gone anyway.
To sum it up, in the face of annihilation, all our petty squabbles, and even our relationships don't really matter. Survival is the only thing that matters. And throwing everything away to deal with the Reapers is portrayed kinda well by the ending.
