Nintendo showed of an exclusive mode for the 3DS version, but the Wii U got none. Since the NFC project should be done for Wii U by the end of the year, and the game will launch late 2014, I think they'll add a mode where you use the Nintendo figurines in some fashion in the console version.
Note that this also explains why the Wii U version comes out after the 3DS version, since they have to wait for the NFC project anyways, and can spend the extra time on development as well.
I do not think this will be their main NFC game, that title remains for something else, but since they said it would be used in multiple games, I think a Smash bros. mode will get it. And be honest, what better way is there to kickstart this NFC figurine masterplan of theirs?