I think Batman V Superman is just the current working title. They've already cast two other heroes, Cyborg and Wonder Woman, so this thing looks like it's probably just going to be a Justice League movie.
I'm sure the heroes will clash at some point, just like in The Avengers, but just like in the Avengers, film makers found a way to level the playing field a bit (Thor's lightning attacks gave Iron Man increased power output, Thor's hammer was absorbed and dispersed by Cap's shield, etc.).
I think Batman's gadgetry would come into play as well as over confidence on Superman's part. Tons of gadgets to perpetually slow Supes down and they've already said that Batman will be an older version of Batman in this movie, so I assume he'll be a wiley veteran hero character.