They've been hinting at this - customising characters on the 3DS for porting to the Wii U - They're adding NFC functionality to the 3DS... I'll try and dig up the links when I've got more time -
(Edit) - In the SSB Direct, Sakurai mentioned there was more about Smash Bros he was going to reveal at a later date - specifically moveset customisation, and how the 3DS and Wii U games would interact.
As an aside, just looked at Le Figaro -
"En fin d'année, nous aurons aussi deux très gros titres, Super Smash Bros en octobre et les remakes de Pokémon Saphir et Rubis en novembre."
Are they talking about the Wii U or 3DS version, I wonder...