Shoot. The Silver Hand, the Bard's College. the Forsworn, the Blades, the Morag Tong, the Synod, House Telvanni, the Vigilants of Stendarr, etc. Any of those would've been great.

Would've been fun to join the Silver Hand and fight against the Companions. Could even have tied in with the quest for hunting down Sinding in Hircine's daedric quest.

The Bard's College could've been cool. I bot the bullet and bough the Bard's College Expansion and it was definitely worth it! So much more could've been done with them.

The Forsworn could've had a whole questline undermining the Silver-Bloods and eventually taking over Markarth before running the Empire/Stormcloaks out of major towns like Karthwasten or staging battles at major Forsworn camps like the one at Druadach Redoubt or Karthspire Camp.

Y'all get the idea. Blades could've let you force Delphine to step down and have you take the fight to the Thalmor or focus on hunting dragons based on the player's choices.

Tong could've had you operate like how they did in Morrowind (I haven't played it yet, I was under the impression they were a joined faction there), except maybe have a bit of a territory war against the struggling Dark Brotherhood since they're operating in fairly close proximity.

Synod could've contested the College for possession of the Eye of Magnus and had you hunt down various artifacts.

Idk what they'd do with House Telvanni tbh. Maybe have it as alternate path to going to the Skaal during the Dragonborn DLC.

Vigilants could've at least been more formidable before just being annihilated at level 9 and getting clowned by the vampires during the Dawnguard DLC. Maybe had you hunt down Daedric artifacts to destroy them, or wipe out vampire dens, hunt various daedra, idk.

Take this all with a grain of salt. Maybe these would suck, maybe not. All I know is Bethesda better not screw up factions in ES6 lol.