WB and Rocksteady worked well together to make the first game, so this will not have a negative effect on the sequel.
Hmm, speaking of other franchises, good call guys. And why stop with Supes or GL? I love (comic) book-based games -- when they're done right. I'm sure you guys know that MUA2 was partially based on the "Civil War" events (and it was fun in its own right). So imagine a MUA-like game, but instead of the Marvel Universe, it's based on the DCU, and instead of "Civil War", it's based on the series of "Crisis" events. Heck, why stop there? They could even include the current "Blackest Night" event! And as DrCLos pointed out, the GL film is comin' soon (hopefully), so why not a game about the Corps? OMG, I think I just came. Hehe, but first things first, I guess. Do another great job on B:AA2 RockSteady, and you earned yourselves some loyal fans here.
With the Green Lantern film currently in preproduction, it makes most sense for Rocksteady to make a GL game next. But first B:AA2! I can't wait! :)