Fate Accelerated Edition is a great system for running supers.
Villains: Accelerated is a treasury of supervillains statted up and ready for action right now in FAE.
Villains: Accelerated contains
Professor Hebanon - Demonic Mad Scientist with a split personality in the tradition of Jason Blood/The Demon and Bruce Banner/Hulk
Megafauna - a fun-loving¸ size-changing villain who lives for the joy of super-combat
Cold-Blooded - ice cold¸ superhuman Godfather
The Interceptor - freelance super-thug who specializes in helping drive off superheroes
Xiphos - Obligatory Badass Super Ninja
Dr. Lucas Westerly - a mad scientist in the mold of colorful characters like Victor Frankenstein and Rotwang.
Hoodwink - a self-styled "revolutionary" superhuman who promises to tear down the existing social order.
Dead Eye - Mysterious scourge of the underworld who secretly is working for one of the city's top crime families