Every Dwemer ruin is infested with them. This is probably going to sound [censored] and I am sure that I am wrong, but could the Dwemer actually be the Falmer that were somehow cursed?

Your answer lies here:

http://imperial-library.info/content/skyrim-falmer-study

They aren't. They just don't like the surface world.

Wouldn't it be cool if one of the DLCs was about venturing into Blackreach to bring the fight to them?