I’m only a casual anime viewer, but most of the ones I remember have the usual conquer the world or revenge plot, or something related to their weird setting. Here’s the closest I could think that matches the OP (spoilers, obviously):
Neon Genesis Evangelion: Gendo Ikari - Enact the instrumentality project to join all human souls into a universal consciousness, and to join with his dead wife.
Elfen Lied: Kakuzawa - Replace humanity with superior diclonius.
Tenga Toppa Gurren Laggan: Anti-Spirals - Suppress and/or genocide spiral races to prevent the apocalyptic Spiral Nemsis from occurring.
Trigun: Knives Millions - Exterminate humans to save plants. This makes sense because he’s a human plant thing who was experimented on by humans, or…something.
For nihilistic kill 'em all villains, that seems more like a video game thing, especially in JRPGs, like Final Fantasy and Kefka – but everyone loves Kefka.
For the anti-natalist villain (kill everyone to stop pain) I can only think of a couple offhand, and they’re from Western video games:
Kerghan from Arcanum
Amon from StarCraft II, though it sounded more like a fig leaf for his revenge against the Xel’Naga.
I couldn’t find a TV trope page for that. If one exists it might be helpful.