Although I agree Doomsday wouldn't be a bad choice either I'm gonna side with SilverWook and say that Darkseid would make a great villain for another Superman movie. There's so much to pull from in Jack Kirby "New Gods" world -- and as far as I know he's a much more interesting villain than Doomsday if only because of his motivations and backstory.

That said, I think he'd be best for a Justice League movie. In my dream world that movie would go like the end of Superman TAS where Darkseid drives Superman mad and he almost destroys the world... that would be interesting.