The easy retcon will be saying that the entire galaxy was not in fact effected as planned by whichever rainbow colored light you choose in ME3.
That gives them an easy out to make it really vague as to how ME3 ends, as there is supposedly no canon ending. So you'll see elements of all 3 endings in play. The game can take place a number of centuries later. You'll probably find a number of characters that are synthetic hybrids in places as a nod to that ending. But with the passage of time, many of those hybrids are gone.
Nobody knows what Shepard did to stop the Reapers, which is actually true. There wasn't anybody around to witness what went down with starkid.
The reapers just suddenly stopped, which is also true. And again, if the gates didn't effect the whole galaxy, there would still be surviving reapers. But the reapers disappear soon after regardless of ending. Were they destroyed, nobody actually cares, they are just happy that it is over. You might even have stories of reapers that suddenly regained their past memories, and those reapers either helped out or committed suicide realizing what they were. This could be the control ending, or once the control center was destroyed, they regained some conscience. So it would be very easy to actually combine these 2 endings. Even if Shepard controls the Reapers, I would think of it as being a Madoka Magica kind of deal where he/she cannot directly contact people. And since the Reapers disappeared, it would be very hard to confirm.
Even the races that Shepard could have eliminated could still appear with proper explanation, just like the Rachni.
We already know that the game takes place in an area of space that is less explored and farther away, and that exploration will be a focus of it. This area was probably not too effected by the reaper conflict. It might even be a different galaxy all together, removing us from the reaper conflict entirely.
It might even have a Star Trek Voyager thing going on, where you end up so far away, you have no contact with home.
It really comes down to this: the Reapers were stopped. And no matter which ending happened, while they were all very dramatic, nothing lasts forever. While some might think of it as a cop out, what it really does is show just how insignificant everything is on the scale of the universe and the passage of time. It ultimately makes you realize just how small we, and everything in existence, really are.