While I don't think the ending is the best possible, at least it wasn't predictable. To me, the ending successfully portrayed the desperation and ultimate futility of the struggle, as well as the baffling alienness of the Reapers compared to the relative kinship of the citadel races.
The way I see it, some folks are mad that it doesn't spoon-feed some neat ending in which the hero thrashes the enemy, gets the girl and everyone lives happily ever after; which would be the laziest writing possible and would deservedly draw ire.
In fact, I don't believe many folks actually stopped to ponder the subtleties of the ending before reaching for the internet hate machine. So the ending is not fantastic, so what?