Just a couple quick things on the conventional victory scenario I proposed upthread:
I like this route, and I'm not entirely certain why they didn't bother to go this way, since ME1 planted the idea that Sovereign couldn't simply attack because it would be too vulnerable. I guess a big problem comes right at the end, where suddenly, Sovereign can basically take on all of the fleets by itself, and Shepard was lucky that Sovereign was dumb enough to turn Saren into an I WIN button.
I like that you like my idea.
As far as the battle with Sovereign goes, I try not to make too many inferences about the lore from cutscenes. The cutscenes can show us a lot of silly things that don't necessarily have series implications for the lore, like Shepard's body surviving re-entry and Jack being able to survive in full vacuum with nothing but a chest belt and a breather mask. In general, the Reapers have been exactly as powerful as the story needed them to be. In ME1, when we need to raise the stakes and make the outcome depend on Shepard, then Sovereign can take on the entire fleet himself. By ME3, when we need to dispense with bad guys quickly, one Cain suffices to take out that giant Reaper turret and a couple of "thanix missiles" will take out the Reaper Destroyer.
My problem with the above idea is this: out of millions of years of advanced cycles, some likely more advanced than the Protheans, none of this hasn't happened before. It also assumes that the Reapers don't have an adaptable Plan B for their only job (that they've been successful at since time immemorial), and that Sovereign was not just partly full of crap during his initial speech in ME1, he was entirely full of crap.
When I proposed this scenario in other places on these boards, I proposed just such a Plan B, which would involve the Reapers showing up but pretending that actually, they really mean no harm to us, and Sovereign was just off his rocker. The discovery by the galaxy as a whole that the Reapers did in fact create the relays and the Citadel becomes enough to persuade many that hey, maybe they're right and we should totally believe them, because imagine all the things we could learn from this super-advanced race. Meanwhile, they're accumulating forces by indoctrinating people left and right. It's left up the Shepard to prove to the galaxy that the Reapers are bad dudes who are full of BS.
This gives weight to the idea that "we evolve along the paths that the Reapers desire," because here, we would have the Reapers explicitly taking advantage of our indebtedness to them. It would also add to the significance of the Rannoch and Tuchanka arcs, since the Geth are the only other faction who know what the Reapers are about, and since the Quarians and Krogan, both marginalized by council politics, might be more amenable to the idea that maybe the Reapers aren't such great dudes.
At any rate, the original ending as it stands made out Sovereign to be completely full of crap anyways. In ME1, the Reapers think that organics are beneath contempt; by ME3, they're actually trying to save organic life from . . . something, I guess.