With the Batman v Superman: Dawn of Justice trailer recently have come out, the big question now is who is going to win? Based on the trailer and the story line, I am guessing it is based on Frank Miller's The Dark Knight Returns comic series and films. The trailer shows much resemblance to the films and comics. The Batman logo is almost identical and the power suit also looks similar.
I am going to guess that the movie will not be exactly like the comics, but I am guessing it is still similar. The story line in the comics is that the United States government sends Superman to take out an aged rogue Batman, because they feel like is reappearance is causing trouble. Superman comes and battles Batman, but is eventually defeated by an arrow with kryptonite on it, which is sent by an aged Oliver Queen( aka: Green Arrow).
In my opinion, it will follow the story to the point that Batman does defeat Superman. Even though Superman is much more powerful, Batman has the intellect, and will come prepared.