Thieves' Guild: Tracking down and reclaiming all the gold/jewels/plans that Mercer Frey made off with. You could then do the missions that Gallus had planned before he died. I'd also like to see something that leads to the Guild breaking away from Maven's influence and becoming its own thing.
College of Winterhold: Something involving the Psijic Order and perhaps the Synod. Lots of stuff there left unfinished that I'd like to see play out more.
Dark Brotherhood: Expanding the Dark Brotherhood's members and more contracts. Can't really think of a new storyline at the moment, especially not one that would be better than the original.
Companions: I'd like to see something around the lines of the Companions going to war with the Falmer to try and finish off what they started millennia ago.
^ this would be good.
Here are some more ideas
Dark Brotherhood: Amaund Motierre comes back (or another member ofthe elder council if you killed him) comes with some contracts to kill high ranking members of the thalmor visiting skyrim.
Vigilents of Stendarr: would act as an opposition to Daedric quests and would raid cults of each Daedra
you could revisit the Imperial city only this time the city and the island it is on would be much larger because tullius gets called to the city for something or ulfric is called to the city for a peace treaty and while you the thalmor try to kill you so you try to get rid of the thalmor in the city.
The thalmor could also have a fort you can clear close to the city



)