Satoru Iwata, speaking with The Independent:

I would say generally that 3D is better than 2D. It’s nice to have good graphics but not necessarily on their own, so I don’t think we’ll present [3D graphics] as one of the key features of our consoles but will probably stick with 3D as one of the minor elements of our consoles in the future.

Even if the inclusion of 3D was a wild-success though, I still have a feeling it would be been relegated to that of a minor feature once the new handhelds come around. It could never be the selling-point twice in a row.