It looks like there is reason to suspect that the next Pikmin game could end up in 3D. In a recent roundtable discussion with Shigeru Miyamoto (Pikmin's creator), Shigesato Itoi (Earthbound's creator), Satoru Iwata (Nintendo President), the gang were all checking out the 3DS. Itoi was in the middle of trying out the console for the first time, when he suddenly exclaimed-
At first I figured they were just talking about the brief Pikmin 3DS still-picture demo (seen below) that was shown at E3, but "scurrying around"? That sounds like more than was shown at E3, or anywhere for that matter. Maybe I was wrong in thinking that Pikmin 3 would be on Nintendo's next home console.
There is a lot more to this roundtable than just that. We also get the scoop on Luigi's Mansion in 3D on the Gamecube, experiments with 3D on the Gameboy Advance, the origins of Nintendo's interest in 3D gaming in general, and much more. The full interview/chat is here if you want to check it out.