I actually want the dwemmer to stay the way they are, it's implied that they reached an higher concept of existance (possibly, higher than the aedra) or simply disappeared.
Either way, I don't think they would be interested in mundus anymore, but some of them could return, maybe as a tiny faction, composed of 4 or 5 really powerful characters that were exploring oblivion when the battle at red mountain happened, just like that morrowind character.
Maybe they could be trying to bring their race back from non existing, or join them whenever they are, and while doing so, they could cause massive cataclismic stuff, that could be the thing that drives the game forward.