3. Brainiac
Even though Doomsday killed Superman, Brainiac remains a better contender as Superman's archenemy. There are a lot of ways for Zack Snyder to go about creating his DC film universe and with Brainiac as the big bad - he could have plenty of creative leeway, and if Justice League would indeed be the sequel to Batman vs. Superman, this wouldn't be a bad way to go. His origins have been changed over the years and he's even survived the loss of his physical body by downloading himself else where. He has been a humanoid alien who is the last of his kind, a completely inorganic robotic iteration, or a combination of organic and robotic. But in the end Brainiac would still serve as his super-villainous self whom is known to be a collecter of worlds. He has been known to miniaturize and bottle the greatest cities of civilizations and then destroying the home worlds. He even bottled Kandor of Kal-El's home world of Krypton. His name should be a clue to his intellectual level and physically he can throw down with the best of them.