In my opinion people are making too big a fuzz about the endings when it comes to thinking forward for the Mass Effect franchise. Sure you could think of different conflicts in the future after every one of the endings and I would be fine with different games showing us these conflicts after each ending (at least I can think of interesting continuations after the destroy and the control ending).
But, I doubt this will happen in ME next, because Bioware has indicated that the next Mass Effect game won't have much to do with the storyline of the trilogy. Yannick Roy's "think of the trilogy as World War I" comes to mind. The original quote:
Yannick Roy: ...If you had three games centered around a group of key soldiers in the US army during World War I and then decided to make a game about another group of people during the second World War, the games could have many points in common and feel true to one another, and you likely would have to recognize how the events of the first war influenced the ones of the second, but you would not necessarily think of it as a sequel. Again, the analogy is not great, but what I’m trying to say is that the ME universe is so rich that we are not limited to a single track when coming up with a new story. ...
Ok, so now how do we get from the ending of the trilogy to a conflict in the future, that is the same after each colored ending? With a "painting" of the starting position:
1) Reapers are gone - one way or another.
2) Geth and Quarian don't play a major role - because of divergent outcomes.
3) Krogan genophage is not a major plot point of the next installment.
4) Survivors in control and destroy are like they were before. In synthesis (if the writers really want to include this ending) the survivors may have new powers, because of "half man, half amazing" - you know? That's the plus, while the downside might be green eyes... 
5) A new threat arises. Because two new races are entering the picture as far as we know, this major conflict seems to be with at least one of those two and not between the existing known ones. What kind of conflict? Could be everything: from a new militant race entering the picture because the Reapers are now gone, to the council races discovering a new militant race on the search for supplies for the rebuild, just to name a few examples.
The ark theory - as I wrote in another thread - just delays the dealing with the endings. But I doubt this theory as the starting point for the next ME, because I think the concept art suggests otherwise. The "citadel-replacement"-hub for example doesn't make much sense on an ark mission.
Discovering unknown races doesn't make much sense in the past, so I think the writers are going forward. The return of the Mako suggests that we are not going fast forward for a thousand years, but rather a short time span. BTW: this makes sense in the aftermath of the ME3 endings, because the biggest possible story differences might come up after a long time (i.e. Reapers returning to be a threat in control?, a new organic vs. synthetic conflict in destroy?) and not in the immediate future.
To sum it up: I don't think it will be much of a problem to come up with an interesting story after ME3s endings while keeping "your choices" intact.
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