I have a feeling that is going to be one of the big choices of the next game. A large chunk of the game I theorize will take place beyond the Perseus Veil, and will involve visiting the Quarian/Geth homeworld and taking part in events that were hinted in the Tali loyalty mission (What you do during that mission may even shape what is happening). You then have the chance to help the Quarians take the homeworld from the Geth, help the Geth destroy the Quarian flotilla, or help them finally put aside the ages of animosity to live together once again as equals. The last mission will be like a massive mixture of the ending of Mass Effect and the ending of Dragon Age.
Just to explain what I mean (and again this is a theory, it may not be like this at all), you will have the ability to do missions for various races, factions, and planets in order to gain further loyalty and support to take out the Reapers, similar to Dragon Age is how you did missions for certain factions in each area that shaped your final army. It will be more organic though in that based on the factions you make loyal, the whole outcome of the final mission can change, much like buying the special shields saved your squad member down in the engine room during ME2. Imagine if you will the Normandy SR2 flying towards the Reapers with the full backing of the Alliance and Citidel forces, suddenly as you are being blasted, the Geth armada or the Quarian Flotilla (or even both!) appear out of hyper-space and join the fray, saving your ass to fight on towards Harbinger (who I assume will be the big boss). Other things you did in ME1 and ME2 will even bring in other forces to fight for you, like the Rachni if you saved the queen in ME1.
I am totally excited at the possibilities. The last mission of ME2 I felt was a great design because of how dynamic it can be, and I can't wait to see how they add to it.