"If you are going to connect Wii U with a home TV capable of displaying 3-D images, technologically, yes, it is going to be possible," Nintendo CEO Satoru Iwata told the Mercury News when asked if the Wii U would support 3-D, "but that's not the area we are focusing on."
In statements reminiscent of the company's justification for not adopting HD for the Wii, Iwata says "when it comes to the home console, it depends upon the availability of 3-D TV sets at home, which, unfortunately, is not expanding enough."
On the other hand, the first Wii very directly targeted a non-core gamer and, as a result, the absence of features that appealed primarily to the early adopting, core gamer crowd made sense; with the Wii U, Nintendo is clearly catering to that audience. "These hardcore gamers are the ones that are looking forward to something brand new, some brand new entertainment," Iwata says. "With Wii U, we will be able to provide them with that."
Considering a massive part of Nintendo's marketing for the still-nascent 3DS involves highlighting its glasses-free experience, we don't think Nintendo is likely to start making 3D games for Wii U anytime soon. But much like Nintendo's do-what-you-want online strategy, it sounds like Nintendo isn't going to stop third-party developers from asking you to put on some 3D glasses.