Exactly. I want this to be the first movie in which the audience roots AGAINST Batman. And I love the character. I hope to eventually land a TV series. He's in my comics, DVDs, and video games. I can't stop drawing him
That being said, Superman should perceive him as a threat, and the film narrative should conform in such a format. When (hypothetically) Batman stealthfully tries to subdue Superman, we should want Superman to be able to overcome him without using deadly force or crippling him.
If they make it a cliche'd 'let's watch Batman kick butt' fight, the emotions will fall flat, and it will be a missed opportunity. I want this Batman to be a menace, only to find out that the character was trapped in an epic misunderstanding. He shouldn't be the main bad guy, or the puppet master. He should be someone who shows up in a few scenes and complicates things. A mysterious stalker figure.
If Superman is framed, then other superheroes will attempt to stop him, out of duty. But what if Batman is the only 'known' superhero out there? By venturing outside Gotham to find superman, he's freeing up other heroes to go outside of their respected territories (this can tie into the later DC movies).
This way he makes the plot more interesting, and adds a real-world element. By having a human exploit the weaknesses of Superman, it can establish the intelligence of Bruce Wayne (but also his paranoia, allowing him to be taken advantage of by a certain evil billionaire).
I'd strongly prefer them to part ways when the truth comes out than team up and save the day.
I know, that's bold, different, and probably unsatisfying. We can have an entire movie of Superman and Batman working together, though.
But a character driven sequel that HAPPENS to have Batman in it would be a rare gift. It would give us the hope of a satisfying buddy movie sequel, while showing the significance of Superman on earth.
In short, it can close out MOS2 while paving way for an awesome sequel, like the Joker tease at the end BB if done right. But I am reaally worried :/