Actually there are plenty of potential plots that bioware have opened up but yet to exploit to the fullest potential, which is kind of disappointing think they may go oops and drop a few a long the way just like they did the dark energy theory about haestrom's sun(ME2 mission where you find Tali).
1) The independent nation of Advent
2) The Quarian Ark
3) The Benefactor, is he good, evil, good intentions but ruthless like a spectre, will he be like TIM in ME2 or TIM in ME3? Is he backing the collective/Reyes.
4) The Kett: The Archon claims to be the genetic inheritor of 1000 species. So technically there could be 2 branches or avenues Bioware could progress this:
a) Kett is evil, you go to their home world find a bunch of new aliens yet to be enslaved or exalted...
b) Kett is like the reapers, truly believing that in order to save their worlds, they need to merge into one strong race in order to repel the darkness that will follow. A little like the protheans who subjugate other species into the prothean empire, but this is a little more literal.
5) The Jaadaan, are they organic? AI based? What are their intentions? To create life seems to be the theme here, but is there something darker? Creating unnatural lives and an army to go up against real organics?
6) Scourge, all we know so far is that they are not natural and that they target remnant technology. Are the creators of the scourge good/bad/order/chaos? If Bioware chooses bad then it is the easy and obvious route, same theme of evil beings giving hell to everyone else... What if they are actually good, trying to survive the Jaadan and in their desperation they created the scourge to counter the remnant threat? What if they are like the protheans sending a sun to supernova just to kill off the machines during the metacon war? Perhaps they are like the leviathans, numbered and dying as well cause their creation, the scourge, affected them.
7) Will SAM carry on riding with Ryder... Will it become like the Zha and Zha'til where the AI controls their host? Will Ryder eventually be controlled becomes like TIM, indoctrinated evil version cum secondary antagonist? Or will he somehow be ousted and then reside within the Sibling and later all out sibling rivalry and war?