I wouldn't be surprised if we had a scene with Superman's hand around Batman's throat, flaring up his heat vision but letting Bruce go, harkening back to the classic line.
(I want you to remember that I 'could' have killed you, but didn't, because I only kill when it's absolutely necessary)
I actually speculate that a similar story to TDKReturns could actually play out with a significant role reversal happening.
Here's a post I made from another thread with my idea for how it could go:
In my mind, it would play out something like this, in TDKReturns, you have Superman who's on the omniscient higher authority antagonist's(US Government's) speed-dial and beck and call while old Batman is the upstart making a name for himself in Gotham and we know how that story goes. In my mind, for the movie it would still have something like that happening, but differently. Superman's the upstart making a name for himself in Metropolis doing the whole "Truth, Justice & The American Way" thing and just being Superman, stopping crime, left right and center and helping workers rebuild Metropolis, and just generally helping people, heck throw in a scene of saving a cat from a tree or helping an old woman cross the street haha. Of course people are somehow warming up to him(for argument's sake let's say the damage to Metropolis wasn't as bad as we thought it was and more people are actually left displaced rather than killed) and the Daily Planet writing glowing reports about Superman. Of course not everyone's happy about the alien, here we introduce Lex Luthor, who takes the place of the US Government as the omniscient higher authority from TDKReturns.
Luthor doesn't like what he sees and feels Superman upstages him at every corner(perhaps show him flipping through the latest issue of the Daily Planet where Superman is pages 1-5 while Luthor's page 10 lol). Luthor flips out and decides to concot his plan to take own the Man of Steel by first framing him for a crime he didn't commit, preferably murder(ala Public Enemies) and of course Superman goes on the run trying to prove his innocence as seen in the comic/animated movie, Lois could help here if she wants. Since no known police can actually take someone like Superman in, Lex uses his connections to a friend in Gotham City(Jim Gordon) who in turn calls in the people's superhero Batman, who supposedly handles an assortment of freaks like this on a daily basis.
The movie becomes pretty much a cat and mouse game between Superman & Batman culminating in a fight in Gotham's Crime Alley ala TDKReturns. So Batman then uses an assortment of different gadgets and traps to stall Superman and then of course releases the Kryptonite(Here Batman would just call it "radioactive meteor rock which simulates your home turf". Batman, being smart could make some analogy to how we are different in other planets like how when Astronauts go to the moon they become weightless etc and reasoned that materials from your home world must soften you up or something). Then Batman grabs and throws Superman through an adjacent nearby building and then a section of it collapses and is about to fall on a mother, father and an 8 year old boy. Superman sees this and with a final burst of his heat vision destroys it into debris ala Superman Returns. Batman looks on and is stunned and horrified about what he nearly did and realises that Superman is not the bad guy. Then the sun comes up and shines on Superman.(Think of it as a form of symbolism, that the night had its fun and now is the light's turn to
take over). Superman uses a burst of speed and swoops down on Batman.(On a side note, the Kryptonite ran out and is out of Superman's system).
*Superman grabs Batman by the throat*
Superman: "Did you realise what you just nearly did?!"
Batman(gasps):"I needed to neutralize you. You scare people, you think you are high and mighty and above the law taking lives as you please, you are no God!"
Superman:"You're one to talk with what you nearly did there!"
Superman:"I want you to remember...Bruce Wayne"
*Batman's eyes widen in horror that Superman knew who he was this whole time*
Superman: "I want you to remember this symbol Bruce, it means hope. My father sent me here for a reason: to be a symbol of hope for tommorow and every day after that in all the years to come. I'm not here to rule over you or act as judge, jury, executioner. I know that now, from first hand, I want you to remember Bruce, I will never kneel before evil."
Superman: "My purpose in life is to protect life and fight for Truth, Justice and the Right Way. If lives are in danger, I want you to remember that I will always inspire hope."
Batman: "I know that now."
*Superman releases Batman*
Superman: "Fight's over"
Batman: "Luthor..."
Superman:"What?"
Batman:"It's Luthor, he did it"