If you chose the neutral option in ME1 (focus on Sovereign), the alien council is reformed, but with a human at the head of it. There are so many ways you can go. I fully expect ME3 to have 3 endings: Paragon win, Renegade win, and Reaper domination. After seeing what they did in ME2, I have to believe they'll have an ending with the Reapers winning.
I wonder if you make those choices to restore/rebuild/help those alien races, but also take those renegade chances to grab all the tech you can, what you end up with?