It pretty easy to see what they'll do next. One day Mario goes for a walk in the castle when he notices a pipe he's never seen before, he decides to go down it to see where it leads. At the exact same time, in a parallel universe, Link is going for a walk in Hyrule field and goes for a quick swim in Lake Hylia. All of a sudden, a powerful whirl pool forms under Link and he is sucked into an ancient pipe hidden under water. Through some strange kind of inter-dimensional fuck-up-ery they both find themselves to be in the others reality.
Meanwhile, by some random chance both Ganondorf and Bowser decide that it's about that time to cause mischief by kidnapping Peach/Zelda again. For some dumb reason the only way for Mario and Link to go home is to save each others princesses.
This actually sounds pretty good. Hang on, I need to go copyright this before anyone at Nintendo finds out. Please, under no circumstances tell Shigeru Miyamoto until after I get back.