I might catch some crap for this from the extremists, but I think the Court of Owls would be really cool for a film. It would roll in the mystery/detective element that I think a lot of us agree has been very sparse in the franchise so far, but also feel fresh and scary too.
Other than them, I would look to: Hush, Black Mask, Red Hood, re-invent the Riddler, Mad Hatter, maybe do something like the Holiday killer, get more into the Falcone family, Hugo Strange, re-approach Catwoman as a villain... Arkham itself could stand to be explored better.
I think I've said this elsewhere, but I also wouldn't mind if they did it as a collection of smaller but meaningful and reflective stories, in the vein of Haunted Knight or Black & White. (If you haven't read those, do it.)
Man-Bat, Freeze done right, and Clayface all would delight me too, in terms of the more 'out there' foes.