I would say that the best ones would be:
Black Mask - Originally a business executive of Bruce Wayne who hates him, he becomes the leader of The False Face Society, a criminal gang that wears masks.
Reasons why not: The masks were pretty much worn by the followers of The Joker, so it might seem like a ripoff.
The Riddler - A man who has a compulsion to leave clues to every crime he commits. He eventually becomes more of a help to Batman, after his original stint as a bad guy.
Reasons why not: Lol, they would have to get rid of the leotard, and just give him a green suit. I would be sad to see his question mark staff go though, that thing is awesome.
Hush- A childhood friend of Bruce Wayne's. He tries to kill his parents, but his mom survives. Bruce Wayne's parents both die, and this makes him jealous and angry at Bruce. Later on, he becomes a scientist who commands The Riddler. The Riddler figures out that Bruce Wayne is Batman and they join forces to kill him.
Reasons why not: None, he is a perfect villain for the next movie.
So, basically, I think that Hush would be the main villain for several reasons. He actually means business (he beats The Riddler within an inch of his life, kills poison ivy in the comics attempting to recruit her, etc.) and is a strong, creepy, complex, and commanding character. Him commanding the Riddler in the movie makes perfect sense too.