Control would make the most sense to me, as the Mass Effect universe is still mostly the same except the Reapers are now oversized galactic versions of the Keepers. Destroy trashes too much, and Synthesis would feel like a completely different galaxy.
Bioware could possibly handwave both Control and Destroy into the same universe if they set it centuries past the end of ME3. I don't see how Synthesis could fit in any way though.