Problems with arc theory
1) Most likely introduce new technology to a level you don't want in ME, especially if it does involve intergalactic travel
2) Carrying off all the different species you want for the story wouldn't be logical. The council is hardly likely to squash Krogan, Quarian, Geth or Vorcha onto their experimental ship(s). Even Volus who could contribute financially would place such a huge additional cost due to their requirements it would make more sense to leave them out.
3) Why wouldn't the ark turn around once the reapers are defeated? They have quantum entanglement so they would know.
4) Could they even get out of the galaxy before the effects of the crucible reach them?
5) The image we have seen resembles Andromeda and that is the most well-known to the public. But why would that happen in reality? Canis Major Dwarf, which the image looks nothing like, is so much closer.
6) Do players really want to play as one of the people who fled the reapers, leaving everyone else to die, rather than fighting them?
It is a somewhat creative theory but I feel it would not have very sound logic. It also doesn't resolve answering the ending and the canonization problem, it only delays it.
If they really wanted to do something like this I think it would be better to do it via an accidental, uncontrollable wormhole like star trek voyager or Homers Odyssey. The people sucked through would be the galactic fleets who were near the relay when the crucible blew.
I would prefer they make a sequel set in the milky way with destroy chosen as the outcome. It is not saying this was best or what happened. It is saying if Shepard did this, then this is what happens next. The Mass Effect setting is more than the races. It includes the places, the individuals, the political and corporate organisations. It includes the planets and moons, the systems and clusters. It includes years of history, conflict, tension and alliances. I don't think they should abandon that.