Well, I imagine the third game will be all about the decisions you make between particular sides in smaller conflicts that will decide who helps you in the larger conflict; basically, the idea behind Dragon Age. So this includes:
-Wrex vs Aria, it's heavily insinuated that they have a past and they will be going at each other's throats again. The winner of this conflict (as chosen by you, of course) goes on to take control of the Omega station and use it as a heavy military base.
-Geth vs Quarians, this is a given, and the winner of this conflict decides who gets control of the Quarian home planet and consequently, which side will support you. A Tali-Legion standoff is inevitable.
-Liara vs Shadow Broker. Insinuated that the latter is the former's papa, this would be an interesting choice between the Broker's richer connections and the loyalty to Liara you have. It's a classic Bioware dilemma in the making.
-Alliance vs Cerberus. This would be pretty fun, especially if you kept the Collector base intact, and would be an interesting way to solve a lot of problems. Either the Alliance defeats Cerberus and takes over their advanced technology, or Cerberus overthrows the Alliance and establishes control over a large army (and in the process, being paid back for reviving Shepard). And depending on how this plays out, there could be an awesome scene wherein Shepard executes Kaiden/Ashley, or even more fun, converts them to Cerberus operatives.
I'm thinking that the game will revolve around these choices (and really, there's a few more that can be thrown out there), and in the end, you will have multiple forces that can be used to defeat a Reaper invasion. This is the "Return of the Jedi" entry into the series, so that gives a lot of hints. Shepard overcomes indoctrination, kills off the main reaper, either deactivates other ships or waits while gigantic army annihilates Reaper remains, and relaxes with a vodka martini after everything.
Just FYI, Bioware has said that this is the last ME game in the original trilogy, and it will be the last to feature Shepard, but it will not be the end of the universe associated with the game. I doubt a "Reapers are successful" ending would be appropriate because I'm sure Bioware doesn't want to replace every race. It'd be fun to see Shepard blow his brains out, though. After all, the only thing that can stop him at this point is himself.