That is a fair point, but there's also too many egos, lawyers, and companies involved. To make a Marvel vs DC comic, you basically just have to have Marvel and DC on board. To make a Marvel vs DC fighting game, you'd need Marvel and DC, and WB and whomever, and everyone would have to agree on who gets in the game, what company gets to make it, who the story will favour, etc. etc., blah blah.
They would have a massive amount of things to work out, like who'd be in it? Obviously it'd have Wolverine, Superman, Batman, Wonder Woman Spider-man and the Hulk along with the other A-listers, but beyond that, who do they add? Both have hundreds of characters with massive fanbases, but a limited amount of space. So obviously not everyone's favorite character would make the cut.
You think roster complaints for MVC3 and Injustice were bad? Just think of this game were made. The roster would have to be no less than 100 to please anybody. Then the arguing over how it should play and who should make it. And silly character arguments like, how would most of the Marvel cast be able to fight against Superman?