There's only one way to go from here: Multiple Villains BUT!!!! Hear me out. Dark Knight pulled it off well and they set it up like the ending of Long Halloween where the freaks basically take out the "normal" mob and set Gotham up for a new breed of villain.
Instead of the whole stupid "we need to team up to steal the minds of Gotham or freeze it so our super plants can breed" you simply make it a mob film where different gangs are tearing the city apart and BatMan needs to stop them. They still have the whole escaped Arkham inmates thing going.
Black Mask = Michael Wincott
Ventriloquist = Christian Clemenson
throw in Penguin as an information man, ScareCrow as a drug dealer (bit of a waste but that's what they made him)
Killer Croc should just be a huge psychotic body gaurd with a ridiculously bad dry skin condition that looks like scales. Shame they already used Tommy "Tiny" Lister in the Dark Knight. And throw in DeathStroke as a masked assasin thats hired to take out BatMan... or as a twist, Bruce Wayne?
and please, no Riddler. He was awesome in the Frank Gorshin and early animated series days but after Jim Carrey, I realised how lame a villain with an impulse to leave riddles behind is. Also, Catwoman is... a cat burglar... how much can they really do with that going up against BatMan in a huge big budget two hours plus picture? Unless you give her some kinda plays both sides sorta deal... which now that I type it, sounds like it could work.
Oh yeah, and have it turn out that Joker was behind the whole thing from Arkham. You can keep him in the shadows in their final dialogue at the end, just have a really good voice guy. It'd kinda be like the ending to Broken City. One of the most underrated BatMan stories ever.