Nintendo has yet to make interesting use of connectivity between Wii U and 3DS, but that doesn't mean we'll never see its potential realized. In fact, the Big N currently has a few projects in the works that will reportedly make excellent use of the functionality.
"There’s no real reason that we haven’t done it yet," Shigeru Miyamoto told IGN. "I guess it just hasn’t really fit into the titles that we have been making and it’s not that we haven’t thought about it."
With regard to connectivity between the 3DS and Wii U versions of Super Smash Bros., Nintendo's Shinya Takahashi had this to add:
With Smash Bros., because the two games have the same gameplay and the same controls, that game in particular is designed where you’ll want to start playing on the 3DS first and build up your characters there, and then transfer that character data over to the Wii U and play with them there.
Takahashi went on to tease a couple of connectivity-centric projects that are currently in the works, saying, "there are some things that we’re working on that we haven’t announced here at E3 that do involve some sort of communication between the Wii U and 3DS."
Unfortunately, the two couldn't say much more beyond that, only hinting that they "are thinking about that with Mario and Donkey Kong."