Mike Gamble is now Project Director at BioWare - What could he be in charge of?

My theory was that the collectors are actually a race that rival the reapers but while the reapers are post-singularity machine entities, the collectors are all about bio-engineering and biological evolution (think roughly Species 8472 from ST: Voyager vs. the Borg). Those two races would have been in a sort of cold war for millions upon millions of years, without either winning a decisive victory. They both keep the cycles going as they both hope it will eventually give them an advantage. While the reapers hope to see new feats to technological engineering from each cycle (and create new reapers by uploading people into a new one of their own), the collectors hope for new avenues of biological evolution to study, to augment their own DNA (hence their interest in all those particular specimens that we read about in Ascension).
ME2 would have been about finding out a lot of this background. ME3 would have been when the war goes from cold to hot. It would have been a three front war between the reapers and collectors with the current cycle races caught in the middle. Your main objective in ME3 would have been to do critical missions to direct the flow of battles, ideally in order to pit the reapers against the collectors directly as often as possible, so they weaken each other (you know, lure the collectors here, maybe destroy another relay to get the reapers to go a certain route, etc.). There would also have been the possibility to fail missions (without a game over), which would diminish your chances for the end game.
In the end, Shepard, with all the knowladge they gathered in ME2 and all the delaying and battle-channeling actions they took in ME3 would put themselves in a position where they force a decisive confrontation, with a chance that all parties might actually wipe each other out. That leads to some negotiations, where Shepard could choose to side with either side or (if the players preparations were good enough) pull kind of a Sheridan (from Babylon 5) and make the reapers and collectors figure their own differences out without destroying our cycle in the process.