I was making a vanilla dungeon overhaul during some time under the name of Oblivion Dungeon Re-Experience, but I never finished it. Still, I think I had some good ideas for vanila dungeons during development, and thought I'd share them with you:
1. A Dark Brotherhood sanctuary for a dungeon. Fort ruins near major cities appear to the best types of dungeons for these. I considered Fort Nomore for example before I stopped making my mod.
2. Daedric strongholds. Basically dungeons that the Daedra have overrun during the Oblivion crisis as bases of activity. You could choose dungeons located at strategic points near cities or major roads and give each of the dungeons a "Plan for Invasion" or "Plan for Attack", hidden deep within. Dungeons like Fort Rayles have a great view over a neighboring city and could be considered as Daedric strongholds. If you were to do this, best to copy the original dungeon, make changes to the copy, and reroute the main door to the copy instead of editing the original dungeon, as this idea requires more than making a new zone.
3. Crumbling Mine and Fort Carmala outside Chorrol. You could write a note to be put in Crumbling Mine about how and why the bandits are digging into Chorrol's sewer system. Perhaps even make the sewer system accessible, with an entry grate in Chorrol. Knowing this would conflict with Better Cities if done wrong, I suggest the entry is placed in Chorrol's northeast corner - that area is left mostly untouched by BC. Another entry to the sewers could be in Fort Carmala, the fort outside Chorrol. A story could be added inside the fort describing the fort as a sewer waystation. If this was done, any Chorrol sewer system you build could be infested by vampires, as the fort itself is.
4. Not every dungeon needs to contain enemies. You could make a dungeon home to friendly NPC's or even a fence (Oblivion is in dire need of non-Thieve's Guild-afflitiated fences anyways). Small dungeons like Garlas Agea or Quickwater Cave are good starting points. In a mod made by a friend of mine, Beldaburo was changed into a home for some pirates stranded on the coast when their ship crashed onto the beach, and included a story. The pirates were (mostly) friendly, and one was even a fence with which you could barter. The first level was inhabited by pirates; the second was empty and a rat pit.
5. Broken Promises Cave. When I was working on this cave, I envisioned it as a witch coven, using resources from the resource pack CURP to fill it with witch items. The witches don't even need to be evil - in Daggerfall, most covens tolerated you and even gave you short quests. It's isolated location from any other dungeons or areas really makes it perfect for any idea that requires isolation.
6. Outlaw Endre's Cave. Make it really home to an Outlaw Endre and his gang of bandits!
7. The following is stuff written by a friend of mine for a mod he never finished:
I do hate to impose upon an old friend but it seems the matter has grown worse over the course of the last few months. Where once the sounds were a rare occurrence it seems now that the moans and groans of Toadstool hollow are heard in the night near constantly now. I pray you and your brave men will rid us of this menace once and for all, and restore peace to those traveling along the path to Bruma...{the remainder of the note is badly torn and stained with something which you would like to believe is wine and which you are equally certain is something far more menacing...}
{this seems to be the remnants of a tattered note. The beginnings are lost elsewhere, likely never to be found}...remember we used to go there, to Toadstool. See how far down into the caves we would go. Used to take us some bottles along, strong stuff from up north at Olav's usually. Even made it to the second level of the cave once. I bet your old ring, the glowy one, is still in that same damned coffin you dropped it in all them years ago. I hope you figure out what's goin on there, Donny...{the note ends here in ragged tatters...})
Include some dead corpses with the notes on them, and you're complete!
I reccomend checking out the mod Nehrim for ideas on how to treat dungeons. The uniqueness of each dungeon in that mod is outstanding.
Anyways, I've got lots more, but I've got to restrict myself, so this is all for now.