The villain always makes a story.
The Joker stole the show from Batman (interestingly, this was true in both 2007's The Dark Knight and in 1989's Batman). Lex Luthor is a heck of a lot more compelling than Superman. Even in John Milton's Paradise Lost, Satan had all the texture and complexity and was far more interesting than God, who was essentially a boring character.
If you want to make your story memorable, make your villain as interesting as you can. Make him or her eccentric and idiosyncratic. Readers will sympathize, and they'll keep reading.