One of the ways I could see it working is if Batman came first and Superman came second. Nolans Batman has to come back out of his self imposed fake death to investigate this new super-man in Metropolis. This eliminates(mostly, kinda, dont think about it so much) the why didnt Superman come to help Batman vs Bane arguements. Also establishes a good reason for the Bat to return. I cant recall if I have ever seen or read about Batman coming onto the scene before Superman in a story but it could work in this instance.