I have a mod that seriously alters dagoth ur. You enter from a small side passage near the Dwemer Library and take a long road. It is very fun. But I'd like to know which mod it is from. Anything come to mind? I could post my mod list, but it is large.
Darknut's Greater Dwemer Ruins comes to mind. It alters the main 6th House bases on Red Mountain to make for a more epic climix to the game. I don't personally use it, however, so I can't guarantee that's it.
Wow, it really does a nice job of making Dagoth Ur feel both like it has been abandoned for ages as well as being the base of a rising evil menace. Good stuff.