I'd like to see Batman figuring out Superman's identity in a similar way to the DCAU version(the little wave Bats gives him at the end is a priceless moment)
EDIT: Cant seem to get the video to work so here's the link...
http://youtu.be/U5nUsa8ZLm4
And I hope they somehow introduce Kryptonite in this movie, so at the end of the flick, after being adversaries at the start and then finally teaming up to save the day we can have something like the exchange in the comics when Superman gave Batman Luthor's Kryptonite ring, showing how much he trusts him despite their differences...