It seems the general consensus that the Bruces do not have a chance against superman alone. But what about together? (Not saying I believe that)
Superman has his mind altered to believe that he needs to get rid of other superhumans but he doesn't rememeber that Wayne is batman. He also has his normal morals but really believes he needs to imprison all superhumans but him.
Bruce Wayne and Bruce Banner go into research and development as a team with all of Waynetech's resources. Banner can hulk out if he needs to. The battle takes place in Gotham city. New 52 Superman. Bruces can use any feats from their history.
Round 1: Bruces get 1 week prep
Round 2: Bruces get 1 month prep
Round 3: Bruces get 1 year of prep