I've been thinking about Nintendo franchises having crossover themes(similar to the crossover outfits in SF vs Tekken), and Mario having another dream would pretty much explain any and every bit of craziness that happened. No real cross franchise characters showing up, but things from their universe would. Solely in theme, as it would still play like a Mario title at it core and be a platformer.
Mario with Pit's wing's when he flies?
Shy Guys with Majora's Masks?
Wart with Soda Popinski's drink?
Koopa Troopas dressed like Captain Falcon...and the winged ones can knee you?
Bowser with a....I don't know...a fucking Screw Attack!?
They could still name it Super Mario Universe
Edit: You know, the Shy Guy bit might be too creepy...