Assuming Bioware ever does a direct sequel to ME3, which doesn't seem to be the case with ME:Next, they've got two options:
The first and probably preferable option in terms of having the least baggage, is to base the sequel on only one of the three ending choices. They can still keep all three endings from Mass Effect 3 canon, but just announce that the sequel only explores the consequences of one of them. Of the three Destroy would probably be the best choice, since it has already done away with the Reapers (a necessity for new villains) and as the fan favorite, it is the least likely to cause the forums or Twitter to go nuclear.
The second is to try and carry over all three endings into a sequel. That would require to some extent ignoring the EC epilogues and having all three ending choices result in a galactic state that doesn't greatly diverge from choice to choice. So the Reapers would likely end up out of the way (or gone entirely) in all three choices. They'd also need to have the galaxy either go partially synthetic at some point after all three endings or the post-Synthesis galaxy to revert to it's pre-Synthesis state at some point. Or alternatively, the results of Synthesis would simply be reduced to few throwaway lines of dialogue, but otherwise be identical. The Geth would also need to exist in the aftermath of all three choices, or to simply play little to no role at all in the sequel.
Neither however is ideal and either route is likely to provoke some criticism. Bioware in effect, painted itself into a corner with the endings of Mass Effect 3. They do not easily lend themselves to a sequel, and while a sequel can be crafted from them it can't be done without generating at least some criticism pre-release. I think the decision on which route to go would require the devs to assess which route was least likely to provoke a backlash. On that note my credits would be on the first option, with Destroy being the ending the sequel explores.
Also it probably goes without saying that Refuse would be entirely off the table and not even up for consideration. It exists only in DLC which means only a small minority of players have ever seen it, and it is nothing more than a slightly more creative Critical Mission Failure. Like the worst outcome of ME2's suicide mission, It has absolutely no chance of ever being the basis of a sequel.