I hope they treat it as a stand-alone, a huge reason BB is my favorite movie is because it stands on it's own legs completely.
That's what annoyed me about The Matrix Reloaded and I know it irritated some Pirates fans during the second one, that twist at the end that was never truly conclusive.
While this kinda sorta maybe happened in BB, it was only a small hook. Those movies basically dropped their endings off a cliff into the next films. I hope TDK, as the definitive Batman movie with the Joker and all, will not make overt references to previous or future films.
It's gotta stand on its own legs.