Despite connectivity between the WiiU and the 3DS already being possible, Nintendo has not utilized the feature very often. In an interview with IGN however they explain that they intend to explore the relationship between the systems much further.
The two systems already are capable of connecting with each other. One of the first things your WiiU will ask you when you set it up is if you would like to transfer a Mii from your 3DS over to your new system. It's a very quick and easy process, suggesting that there are no issues that are keeping Nintendo from exploring it further.
While not based directly on connecting through the systems, you are able to also have your Nintendo account connected to both the 3DS and WiiU. This enables you to manage your funds from either system, and makes buying and registering games much simpler.
With all that said, we haven't really seen the feature implemented in any games. The newest addition to the Super Smash Bros. series is supposed to be big on connecting the systems, Shinya Takahashi of Nintendo told IGN.
“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.”
The relationship between both the Smash Bros. games was already pretty established however. So what else does Nintendo really have planned for us? Well, according to Shigeru Miyamoto and Shinya Takahashi, there are more games to come.
They didn't say much, but Takashi did mention that “we are thinking about that (system connectivity) with Mario and Donkey Kong.” They did not specify whether that meant new, separate games or if they were talking about the Mario vs. Donkey Kong puzzle series.
It does at least confirm that Nintendo plans to further explore connecting their two systems. With WiiU sales steadily increasing and the 3DS already pretty well established, this is certainly good news for Nintendo fans.