Johnny Novgorod said:
I don't think Batman should ever be able to beat Superman, period. Unless he goes skinny-dipping in liquid kryptonite or something like that.
My answer to this as a major nerd is simply to point out that Superman's greatest enemy is Lex Luthor who is an ordinary human. Lex has actually beaten Superman on a few occasions (and come bloody close a whole lot, as that is the whole point of an arch-enemy and the dramatic tension in their battles)), where he has needed assistance, or Lex has needed to give up the victory for some reason or other.
Strictly speaking if it was a straight fight between Batman and Superman, then no, Batman wouldn't have a prayer. On the other hand if Batman is presumed to know as much about Superman as Lex does, and has time to plan and take the initiative, then in theory he could beat him through super-science and the like. Granted in acting this way Batman would be acting as more of a mastermind than in a traditional "Batman" fashion, but he has the capabilities.
In the "Dark Knight Returns" the whole thing was leading up to Superman throwing the fight (apparently going down right before Bruce's heart gives out). Superman points out as the climax he knew Batman wasn't dead, and apparently he could have gotten up an finished him at any point, but chose not to.
That said, in theory, if he had enough time to get ready, Batman probably has enough science and technology to build a battlesuit able to go toe to toe with Superman, Lex has done it, and typically uses one in games and such where he shows up to do action. "Luthor" the good version of Lex from a parallel reality also uses battle armor, and is able to continually survive attempts by that world's Superman and Justice League to annihilate him.
If they really wanted to get cheezy about things, they could always have Batman show up with Kryptonite powered battle armor. In DC comics there is a cyborg called Metallo whose one big claim to fame is that he has a tendency to take down Superman due to running off of a Kryptonite power supply. In movie style when they introduce Kryptonite (assuming they plan to since I'm guessing that will be a plot element to equalize things) they could always drop the Metallo name by having it be the name of the project/development code name Batman bases his armor off of, assuming they go in that direction. They wouldn't be using the character, but it would be a nod to comics fans, and a reminder that it's perfectly canon for things like that to work against Supes.
Of course at the same time, my basic opinion is that if they want to have Superman threatened by brains, planning, and technology, someone should just do Lex Luthor right (who classically is a mad scientist himself). That doesn't get as much hype as Batman Vs. Superman, but honestly given that I can't think of a single really good Lex Luthor who struck me as being a Superman-Level threat in the comics throughout the live action cinema, it's a big part of the mythos that would carry a lot of weight when it's done right.
At the end of the day as far as capabilities and skill sets go, Batman and Lex are very similar. It's just that Batman takes a direct, hands-on approach and does stuff himself, Lex can fight with gadgets and stuff when he needs to, but prefers to stay behind the scenes or not get directly involved, and send minions to do his work for him. Both are ungodly rich, both are scientific and technological geniuses (who also employ other geniuses one way or another), and both tend to be very dangerous in a personal confrontation. Batman is doubtlessly better in a straight fist fight, but Lex is the kind of guy whose likely to have a personal force field and pocket death ray at any given moment (in RPG terms there would be huge overlap, with some slight differences in how they spent their points on a personal level).
