I'm sure a Marvel vs. DC film would make so much money that Disney could finally fulfill its destiny of purchasing all of Florida and the lower half of California, while DC could lock Christopher Nolan into an unbreakable contract that forces him to make Batman movies until he's too old to breathe. But the biggest problem wouldn't be the fact that the movie would eventually be passed through the hands of about 45 screenwriters and script doctors, or that it would take a decade to negotiate all of the contracts. It would be that there's no way to make it satisfying. Because to satisfy at least half of the people, one side would have to gain a definite victory. And this would leave the other side shrieking "NUH-UH" into the night sky.
In 2001, when World Championship Wrestling folded and was absorbed by the World Wrestling Federation, people expected a clash for the ages. It was finally happening. All of the fantasy match-ups that we'd debated for years were going to come to fruition. They just had to. Goldberg vs. "Stone Cold" Steve Austin. Sting vs. the Undertaker. That Guy Who Dances vs. That Other Guy Who Dances. Instead we got a parade of match interferences and barely any solid victories in which one top star beat another. The same thing would happen in Marvel vs. DC: The Movie. Sure, you'd delight in watching Captain America squash the Penguin, but the minute it got to Iron Man vs. Batman, you'd end up with a "But if we work TOGETHER, maybe we can beat GALACTUS" finish.
Superheroes joining together to stop a greater evil sounds neat, but only after I've watched Deadpool kick the bird shit out of Nightwing. I'd want at least one movie dedicated to that latter scenario, and that's the movie that we'd never get.