My mind keeps going back to the scene where Batman has his boot on Superman's neck, ready to kill him. I really don't like the whole "Martha" thing.
I think it would've been better if, instead of Batman killing people throughout the movie, the audience is told that Batman doesn't kill period. But watching Superman and Zod destroy Metropolis, his tower, his employees, and seeing how dangerous and unstoppable a Kryptonian is, he decides to break his most important rule to protect the planet. Maybe have Bruce and Alfred debating if it would be right to kill Superman. I think Bruce's motivation is pretty good in the movie. Even if there's a 1% chance of Superman going bad, with how powerful he is, treat it as an absolute. And if this is an older Batman, hes seen good people go bad before, like Harvey.
Then we get to the scene where Batman won. He has Superman pinned under his boot, ready to stab him with the Kryptonite spear, but he just can't do it. Seeing Superman defeated, sweaty, and bloody, Batman sees him as a human and he just doesn't have the ability to kill him.
I don't know how they would work together after that point. But even in the movie it was dumb. Our moms have the same name so lets crack jokes at each other even though we were trying kill each other like 30 minutes ago.