3. Lex Luthor
This is a touchy subject for many Superman fans. While there is no denying that Lex Luthor has long been Supes' greatest nemesis, fans hoping to see a successful franchise see him as the kiss of death. Images of Gene Hackman and thoughts of absurd real estate schemes haunt our nightmares. But for a character that has been done and done again, he's never been done right in the film universe. I could imagine Warner Brothers taking a character we think we know and making him something we genuinely fear (kind of like what they did with the Joker). While fan backlash would make this presumably unlikely, I think there are a multitude of good stories here that may just be too good to pass up and may also pleasantly surprise us.
2. Parasite
By most accounts, Parasite is a C-list villain. With the power to temporarily absorb energy (and superpowers) of anyone he touches and use them for himself, Parasite has been used sparingly, relegated to the animated series and one-page mentions in the comics. However, after the earth shattering events sure to take place in the Justice League film, Warner Brothers would do good to give Superman a smaller villain who could still stand toe to toe. And with Parasite as the main villain in Superman: Earth One Vol. 2 (a series that Man of Steel seems to be drawing inspiration from) we may see this particular baddy get his time in the spotlight.