From new Famitsu:
3DS and Wii U stages and music are completely different. 3DS is being created as a "portable" version, and Wii U version is being created as a "home console" version, so we will see some differences in that way. It isn't trying to be a super similar game on both consoles.
There is nothing like the SSE story mode. Instead, they are trying to do something more focused on character collaborations of their all-star cast. For the 3DS version, they are planning on having the usual versus mode, plus another completely different way to play.
Now it is the time my hype imagine a 3D adventure Ocarina of Time style mixing Fox, Kirby and Zelda and I realise that the game will never fullfil my hype =(