I think taking Batman to a more Sci Fi level is obvious, with the JL movie coming. But the fantastic elements.. I don't know. I did, however, really like the Arkham games, and something in that direction might be cool. Toning the fantasy down a lot tho, but still. I'd love to Killer Croc, but obviously toned down. not too much tho, still needs to look menacing, monstrous and reptilian. Not so sure abut Clayface and Man-Bat x]
I'd also like to see the Riddler, but not related to the main plot. I don't really see him working as a main villain, more of a side story.. Would be hard to write something like that into a movie script, though..
All in all, I think Mr Freeze is the most obvious choice. He's the main villain that fits best into the JL world, imo. The public also love a tragic villain, regardless of how much it has been used! Would have to tone him down as well, though. Probably mostly refer to him as Victor. Perhaps Mr. Fries?! A single cold pun, and the film is dead!
And the Joker eventually, but not as a main villain. It would be so awesome if they made a film with, say The Black Mask and The Penguin, and then, in the middle of the film, The Joker strolls in unannounced and f**k s**t up for everyone! This could be so great if they managed to keep him being in the film a secret until release!