I hope that they make a sequel, but I REAAALy hope it's not back at Arkham. While I loved it, and it's definately one of my favorite games, I have to say that Arkham itself is pretty much a character of the Batman franchise. However, Gotham city is a huge place and they could pretty easily sanction off a part of it to serve as a map.
I'd like to see some of the villains not featured in this one, such as Two-Face, Penguin, Firefly, ect. Heck, it'd be cool to see the Riddler escape Arkham and take the Joker's role as the main villain.
I'd love to see what they could do if they were given several buildings, the Batcave, and a few streets of Gotham. That "crime alley" level is awsome enough as it is. I'd like to see what they could do with more levels like that.