Warner Bros. has confirmed that Scribblenauts Unlimited will feature various Nintendo characters, including Yoshi, Peach, Luigi, Mario, Link, Zelda, Epona and a Goron. You will not be able to modify these characters, but items such as mushrooms and karts will also be available, which sort of makes up for that.
The characters are also exclusive to the Wii U, since:
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.
In the big scheme of things, it might be a small addition, but it’s still a neat one.