@Skinny- Personally, I wasn't fond of Nyarlathotep as a villain. I feel like the fact that it was basically a game to him made him a fundamentally worse villain. Hazama was a little too edgy and whiney for my taste (I know, he had every reason to be, it just annoyed me).
Do we count Dagda as a villain? I think he was pretty great, as far as motivation and execution.