I read a little on a blog attached to the ME wiki page and I'm glad other people also thought that it was odd that the Normandy was using a relay when it was supposed to be in the fight on Earth. There's no way Bioware could defend that, it just absolutely makes no sense. They also said there's a sound file that Seth Green recorded where he says, to Cortez, that he doesn't want to miss the party. I'm assuming a victory party. It was cut in favor of the "kick the fans in the balls" Normany gets stranded ending.
I think they need to scrap everything after the scene with TIM in the Citadel. The Crucible kills the Reapers, the Citadel and Relays remain, and the Normandy rescues Shepard. Anderson can still die because that helps the sacrifice part, and it was a touching scene between them IMO. I think the Reapers, as intelligent entities rather than puppets, are cooler anyway. Scrap the whole AI that controls them and give the Reapers their own agenda or leave it a mystery.
People also mentioned that the Turians can't survive on Earth because of their biology so they would die after the food on their ships ran out. So if your Garrus survived, it was a delayed death sentence. Hooray for winning!