Fighters Guild
Mages Guild
Thieves Guild
Dark Brotherhood
Psijic Order
Antiquarians (do they have an actual Storyline? I haven't done antiquities yet)
and add Vampire and Werewolf questlines.
maybe a couple of Vampire Lord/Blood Scions (Like the Guy in Wittestadr, and the Ravenwatch Folks, for example), and want to establish a Haven of some sort for all Vampires as a base of operations, and a Council of Vampire Houses or something. Werewolf storyline could focus on you establishing your own Pack or joining a Pack that you meet.
Or maybe hostilities between Vampires and Werewolves, with each questline telling the story from the Vampire or Werewolf perspective.
Fighter's Guild faces some new large scale threat, like maybe a foreign army of some sort.
Mages Guild has more Daedric shenanigans, with a different Daedric Prince this time. Or maybe some long lost deep dungeon is discovered and the Mages Guild sets out to explore it.
Thieves Guild tries to move into Taneth (or somewhere else) and establish a new base so they don't have to live in a Cistern anymore.
Dark Brotherhood - Naryu has a writ on her from the Morag Tong because of Balmora. You find her near death, you take her to the Brotherhood sanctuary and save her. Speaker Terenus agrees to spare her life despite being a Morag Tong, and she reluctantly joins the DB cause the Morag Tong want her dead and she has nowhere else to go. Terenus allows this, on the condition that you and her use her knowledge of the Morag Tong to work to establish a DB Sanctuary in Vvardenfell. (Of course you do most of the work cause...well, she really can't show her face in Vvardenfell). Naryu comes over to the Sithis side by the end of the questline and becomes the Matron of the fledgling Vvardenfell sanctuary. or something.
cameo appearances by Characters from the previous questlines, but a focus on introducing new characters.
something like that.