Although the studio is listening to pitches, and asking writers to use a different main villain (although it is certainly possible that we could still see Luthor in a minor role), they haven't yet decided on any specific script or villain.
Warner's seems committed to making Superman into as viable a franchise as Batman is, and it is true that the film responsible for re-inventing Batman, Batman Begins, didn't feature any of Batman's most well-known villains. So, maybe focusing on a villain like Braniac, Metallo, Darkseid, Doomsday, the Toyman or General Zod would work well for the film.
It is worth noting that Kevin Spacey, who played Lex Luthor in Superman Returns, has gone on record as saying that he'll be back for the sequel, tentatively titled Superman: The Man of Steel - which seems to contradict this report. Keep reading SuperheroFlix.com and MovieWeb.com for more news about the next Superman film as it becomes available.
Man of Steel was released June 14th, 2013 and stars Henry Cavill, Amy Adams, Michael Shannon, Diane Lane, Russell Crowe, Antje Traue, Harry Lennix, Richard Schiff. The film is directed by Zack Snyder.