Batman as "The Unknown."
One of the central tenets of any "Batman and Superman meet for the first time" story is that, at first, they are at best extremely suspicious of each other. Batman is the shadowy vigilante with a terrifying reputation. Superman is the idealistic Boy Scout who works in the light. Superman thinks Batman might be a psychopath, Batman thinks Superman is naieve at best, and has ulterior motives at worst.
http://www.youtube.com/watch?v=F90nxOlsm1s is a great example.
So, in this movie, instead of seeing two actors and characters we know and love, Batman will be an unknown, and so the conflict and be ratcheted higher. (As opposed to the Avengers, where even though they bickered everyone was kinda friends).
I'm not saying your concerns are wrong- actually, this will make people focus on Batman EVEN MORE, which means he better damn well be good.