I've finished the game on the PC, and I'm playing through a second time on my XBox. In that second game, I've just gotten through the end of the Geth/Qurian confrontation. Here's my proposal:
The people who wrote that part of the game? They're awesome. The moron who wrote the end? He needs to be removed from the Mass Effect franchise, post haste. Having done that, have the people who wrote the second act give us an ending that makes sense. That doesn't mean a "happy" ending, btw - it would be entirely reasonable for the ending to be sad.
But it should make sense.