If that's the case we might as well rework the entire universe, then it's not even an AU anymore, is it?
I mean, since you're the main here, Archie, I'll leave it up to you but we have PLENTY of options
We could go as planned originally and simply make an AU without Reapers
We could go with no canon characters but the story could be extremely botched
I mean we can also do an offshoot where Sovereign really was the last Reaper
Or one where the Collectors were created before the Protheans destroyed the Reapers
But since Shepard, the Normandy and its crew, Saren, the Geth, the Collectors, Cerberus, and the Reapers are all extremely vital to the story, a lot of things change if even one of them is taken from the story. Imagine removing two.
EDIT: If my response seemed intimidating, I'm sorry. I'm moreso trying to put things into scope than discourage any further planning. This could succeed, but it is a great undertaking. Having people playing the game right now and defaulting members of the fandom like Grunt is a great way to make this have good perspective. That said, I'm eager to work on this, and I hope my ideas and propositions can help this RP come to fruition beyond the expected scope of a roleplay.