Looking at this ARKCON debate, I have a feeling it might related to the Next Mass Effect, and makes the ark theory somewhat more convincing, but still uncertain.
I mean, one thing we can all agree on is that if a sequel was made, we would prefer if it didn't affect our personal ending to ME3. Some wouldn't mind, others would, but obviously it would be best if they could come up with a solution that avoided this problem.
At this point, there are basically 4 options that I see for a sequel:
1) Canon Ending (Destroy would probably get the most support for this, but I see Control as a more likely scenario. Reapers leave known space, and everything will be as it was before. Geth and everyone alive.) I could see this splitting the fan base. Some wouldn't mind, others would be up in arms, especially since the trilogy tried to minimize canon decision as much as possible and leave the choice to the players.
2) Retcon and ignore (basically say something like ''Oh, the effects of the crucible were only temporary, refuse was never canon, synthesis wore off, etc.) This one would cause the most outrage, at least I think
3) Reboot (basically say the Shepard trilogy never happened). I am not a fan of a reboot honestly. Disregarding the original base and formula of such a successful franchise might cause issues for a sequel, particularly if they start tampering with the lore to ''fix it'' or have a loss of focus in terms of direction.
And then there is the final option that has been debated time and time again.
The ark theory.
Honestly, I don't see why this one would cause such an outrage. It pretty much addresses all of our major concerns. Here is how I would envision it:
Midway through ME3, when things are looking dire, the Council organizes a special project for the sake of survival. This is even hinted at by the Asari Councillor after Shepard loses on Thessia. The council decides to organize a covert operation to save as many species as they can. They appropriately entitle is as ''Operation Arkcon''.
It would consist of making a ship, or group of ships, with as much variety of technology, species, history, etc. and sending them past a deactivated mass relay in the direction of empty space, in the hopes that they would find a safe heaven and avoid detection by the Reapers. This helps us address the ending problem. Since they will be way past relay range, the effects of the endings will not reach them, and thus we can have a Mass Effect experience like the one we've been used to, only in a sequel format.
Once on route, one can formulate many possible storylines. One I think that would work is the following.
Following a long trek, maybe a few decades, the ark finally arrives in a new uncharted system. This fits with what we know so far, and what Casey said concerning ''exploring a new region of space''. This also highly plausible, since as Liara once said, there are still so many unexplored regions in our milky way because of the fact that the council has forbidden opening new relays for exploration ever since the Rachni incident. Speaking of which...
This would allow us to incorporate the new species we've heard about. It would also make sense that we haven't discovered them yet, because even if they did try to activate their local mass relay, it's partner relay must also be active. Because they are isolated in their own system, they remain undiscovered and evolve their own way.
Finally, once the council species get settled, there is a first contact with these new races. Then from there are many possibilities for the game. Set it a few hundred years in the future and have a mini-cold war brew between the various species. Set it just after the ark's arrival in uncharted space and have the protaganist be one of the first explorers of this new region of space. Many possible paths, and definitely room to expand or make even more sequels.
That's just my opinion. I feel that it's the best path, but I guess only Bioware knows what they think is best. I just hope we get an incredible Mass Effect experience. That's my first priority. How they deal with the ending is secondary.