Villains who's main goal is genocide

Zanza (Xenoblade Chronicles. He created life, let it play for a while, and then destroyed it to start again)

Lysandre (Pokemon X and Y. He wanted to kill most of human life for their greed. And all pokemon, which he was less enthusiastic about)

Diesel 10 (Thomas and the Magic Railroad. He wanted to kill Lady, because that would cause all other Coal engines to die alongside her)