To me, the best way of including some form of connectivity would be like the few games on the Gamecube that could link with the GBA. In those cases, it was some little bonus or mini-game. In the two Sonic Adventure games you could move your Chao between the Chao Garden and a temporary Tiny Chao Garden (or a perminant one if you had Sonic Advance). In Animal Crossing, you could link to the GBA to meet Kap'n and access the tropical island. Zelda: Wind Waker had the Tingle Tuner which allowed you to participate in some exclusive side-quests and get special items. I believe that even Phantasy Star Online had some form of connectivity.
With the Wii U and 3DS, instead of making games built around the idea of connectivity, just include a bonus feature. If it's a mini-game, it could be downloaded to the 3DS from the Wii U game as though it were an eShop game. For example, if it was the next Sonic game for Wii U, you could download a Chao Garden to your 3DS which will be perminantly on your 3DS Home Screen and accessable and playable whenever you want. If it was more like the Tingle Tuner in Wind Waker, likewise, a Tingle Tuner App would be downloaded to the 3DS and you'd have to launch it on your 3DS to use it in conjunction with "Zelda U".