I don't think there's any need to bring back The Joker. They left with a pretty straightforward motif: The Joker will always be around. Evil in Gotham City will always exist. It will always be Batman's duty, even outside of what is being filmed, to keep Gotham City in order, which is what The Joker ends up representing.
Now, for a villian in the third movie, I think they could do a lot with The Riddler in terms of storyline. The only problem I have with him is that he is a little too similar to The Joker. They could still bring back Two Face, but they may have used up all of his charm in this one. I don't know how they could do The Penguin again without it being too similar to Batman Returns. Mr. Freeze could be done in this series maybe. Probably Baine as well.
I personally would either go for The Riddler or the return of Two Face. I think they left the Two Face thing open to interpretation just so they could write him off just in case. Although I don't think we would want them in the same movie and have another Batman Forever now would we?
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