I'm going to be a little weird and say my favorite super-villain is minor side character Accord from the web serial Worm.
He's a super-villain with some OCD like tendencies whose super power is (as far as I can tell) the ability to understand complex systems in an intuitive way which lets him "improve" them to his liking. Basically he has a very focused sort of super intelligence.
His backstory is that after he got his powers he drew up plans to end world hunger and dependence on non-renewable energy, but no one would listen to him. He got so fed up with things that he turned to villainy in order to make things change, lol.
Too bad he's barely in the story and he (rot13)trgf xvyyrq bss cerggl rneyl, but he's pretty interesting I think.
