A couple days ago it was revealed that Nintendo characters would be available for you to use in the upcoming Scribblenauts Unlimited. The thing is though that these characters are exclusive to the Wii U version. Now we have 5th Cell explaining why they are not present in the 3DS version:
“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…only the Wii U and PC [versions] remained and obviously Nintendo would only want their IP on their platform.”
Basically the Nintendo 3DS version of the game was already finished and moving on into the manufacturing stage before Nintendo allowed them to use the characters.