Considering how the writers seem to have a fear of making an arkham game without joker any other answer is almost funny.

While Joker would be the obvious choice since he's the Joker, I'm going to go with Scarecrow. Unlike Joker, Scarecrow actually won (despite being caught right afterwards). He exposed Batman's secret identity to the world and forced him into hiding.

I'd have to say Joker since I like the symbolism behind him. Like how Joker and Batman are two sides of the same coin.

Always the Joker