One possible thought for 2 of the 3 endings that would make the back story make a little more sense - the Reapers are actually storage units for the harvested races. Actually, with a little work, this is OK with all 3.
All of them clearly store the genetic material of the harvested races. They even maintain their intellects in the gestalt form. Indeed, Harbinger talks about Shepard's resistance being 'wasting lives.'
What if the entire plan was to keep the genetic material and diversity of life viable until the endless cycle of organic/synthetic war could be ended.
The 'death' of the reapers could bring forth hundreds if not thousands of new races. And that would make a hell of a story. The reapers could become breeders, creches for the dissemination of the new races.
Indeed, both the control and synthesis options could include these as well. Under control Shepard could realize the purpose of the Reapers, and after helping rebuild the shattered civilizations could trigger the reseeding. Then create a new body for himself, restoring his mortality.
And the synthesis option this could happen as well. You could go with the synthesis option, which as we've seen isn't really that big a deal, as Shepard himself is part synthetic since ME2 with very little change in him.
Or you could open the way that the synthetic element allows for even larger scale indoctrination by Leviathan, who understand the technology, and were setting this all up to recover their own faded dominion over the galaxy.
Anyway, positing thoughts on how the story could continue.