While 3DS games are always going to have some degree of 3D in them (hence the name of the system), Nintendo seems to realize that the technology is still just a fad for regular TV owners. According to an article on Joystiq, "the Wii U will support 3D televisions but Nintendo itself won't be focusing on making 3D games."
While the fact that the Wii U will support the tech at all seems to be more of a concession to hardcore, technology early-adopters, it does show Nintendo's willingness to give third-party developers the room to create the kinds of experiences they want. Still, whether the 3D effect is hands-free or not, I still feel it never adds anything meaningful to the experience. Once life-sized hologram games start coming out, then I might jump on the 3D bandwagon.