However, the 3DS version of the game won't be getting in on the action. While an official explanation for this discrepancy wasn't provided by Warner Bros., Jeremiah Slaczka, creative director over at 5th Cell, explained that it was a matter of 'timing'.
To quote IGN:
“Timing,” Slaczka told IGN. “The 3DS version was already finished and moving into manufacturing (cartridges take longer to produce) by the time the deal was signed with WB & Nintendo.” After the deal was signed, Slaczka adds that “only the Wii U and PC [versions] remained and obviously Nintendo would only want their IP on their platform.”
As for other franchises, Slaczka added that "it's just Mario and Zelda for now" but that "there's plenty of characters and other goodies to discover within those universes." He said that "many unique objects" are included from both franchises and that the characters are "just for fun. Though it's up to the player on how they want to solve a puzzle, so it's possible they could use Nintendo characters to do it."
Slaczka also noted that "this deal happened pretty late in development so we didn't have time for locations" and once again confirmed that the Nintendo characters cannot be modified by adjectives, as "understandably Nintendo is cautious about letting other games use their IP. So for now their characters can't be modified."
You can hang out with Mario and friends when Scribblenauts Unlimited releases on November 18.