I admit I like the grey vs. grey as well, and I do plan on multiple outcomes. But I do think I will put a 'more right' option in as well, even if it has the player guessing if it really was the correct thing to do.
I wouldn't focus on the villainy aspect of this too much though.
I've definitely been considering something dwemer related, but at the same time I can see dozens of dwemer quests popping up when the CK comes out. I've been leaning towards something a little more alien.
You can just use the already-existing factions and people's pre-existing leanings to muddy the waters.
Look at how the Imperials vs. Stormcloaks debate goes - before the game was released, players favored Stormcloaks 2-to-1, but now, a recent thread I was in actually favored Imperials 2-to-1. The more argument happens revealing how involved the Thalmor are in starting the Stormcloak rebellion, the more people generally side with the Imperials, but at the same time, people had a natural inclination to go for the underdogs and the rebels, just by default.
If you want to really shake things up, make some group that is normally hated (oh, say, Reachmen) into the ones that bring about the best outcome, while the groups that the players would naturally have the most affinity for (like, say, a survivor of House Telvanni) would have the most disasterous consequences for the broadest number of people.
It only took one optional quest to turn the fanbase against the Blades, though...
Anyway, if you don't want to go dwemer, go for some esoteric metaphysics on how the towers work. Make something having to do with how The Throat of the World works as a regulator of the laws of physics of Nirn, for example.