1) Who are the Jardaan, why did they make the Remnant, why did the Remnant design the Angara, who was attacking them? Really everything revealed after you find 'Meridian' is a huge cocktease for a bigger storyline which almost seems superfluous because...
2) What is the Ket empire? We see a few communications from the, clearly much bigger, Ket empire which would seem to span most of the actual Andromeda galaxy and is something akin to what might happen if the Zerg and the Borg had kids. The big bad guy we dealt with is actually just a minor functionary in the overall plot. I was fully expecting there to be some revelation that, away from the front lines of genetic conquest, the Ket civilization was actually quite nice. The few Ket we speak to seem to think becoming Ket is really a positive thing afterall. What if it is an analogy to marines who blow up small villages and yet still don't understand why the residents of those villages have issues with America.
So we have two BIG galaxy-spanning plot elements that really just get started in many ways by the time we reach the end of the current game.
In addition we have a bunch of smaller things:
-- Ellen Ryder : who will presumably be brought out of Stasis at somepoint. Perhaps she can take care of your kid in a sequel as you go off to save the new galaxy.
-- Quarian Ark: they did escape the Milky Way and are out there but are warning people to stay away
-- Jien Garson: murdered after arriving because she knew too much about ...
-- The Benefactor: mysterious entity who swooped in to fund the Initiative in order to escape the Milky Way
-- Milky Way: No matter what happened in your universe, something took place with the Reapers shortly after the arks left and Ryder has the reports of the Reaper attacks all over the place.
Surely a couple of those can be mined for DLC, but the big issues are the sort of thing that would be tackled by a full sequel.
