In this article about an Iwata Asks published back in 2011 -
"What Sakurai hopes to do is have the 3DS version of Smash Bros. allow players to build up their character through battle and rewards, then take their custom character to the Wii U version to face off against everyone. He feels it could be nice if they can make the "personal" portable space and the stadium-like "public" console space mesh together."
In the Smash Bros Nintendo Direct last month, Sakurai talked more about customising your characters' abilities, and hinted at increasing their capabilities - which could then be used in local play and Fun Mode online, but not in Glory mode. He also teased a connectivity between the 3DS and Wii U versions.
(Edit) And this pretty much confirms it will be possible, although it seems the NFP compatability between 3DS and Wii U won't be available until first half next year.
