Please note that there may be a few spoilers so read at your own risk if you have not completed the game.
Idea 1. The Protheans still exist:
In ME it is revealed that the Conduit is a mini mass relay, so we know that the Protheans were experimenting with mass relay technology. It took the Reapers 600 years to wipe out the Protheans, they would only need a couple of million people (Perhaps a 1 colonized planet) to survive (Remember there are only 17 million Quarians in the Flotilla). The Protheans were also more advanced so we know that they could do it.
Idea 2. Best Seats in the House:
I watched a commentary on GameSpot (Tried find the link but I seem to have lost it). They said that the ending would have been better if they had ended it with Anderson and Shepard watching Earth from the Citadel. I like this idea with it going to a cut scene of the Crucible firing and the Reapers getting destroyed. Depending on player choice and Effective Military Strength.
Idea 3. Failure: