I want it to be like Game of Thrones. I'll set the scene
The Protheans survive through Stasis Pods and establish a Galactic Kingdom but the Reaper threat is still out there despite now becoming a myth.
Relations between humans and protheans are frosty at best and its up to you to end the conflict in some way.
It would work because:
a) its an alternate universe so the endings are moot

moral choices and melodrama (things that Bioware does best)
c) Its plausible for these events to occur
d) we can still have Garrus and Wrex in some way