You'll still have the capability to use the Wii remote motion controls including Wii motion plus. I'm not surprised Pikimin jumped a generation. You simply have to look at how Nintendo approaches development and how their developers think, especially in the case of Iwata and Miyamoto. During development Miyamoto will completely throw out a game if it doesn't meet his expectations or he wants to add new ideas and those ideas conflict with the current version of the game. This can be seen as the result of the new art direction found in Skyward Sword motivated in part after adding Wii motion plus functionality. With Pikimin it may simply be that the Wii's hardware wasn't capable enough to do what Nintendo wanted thus why this game was continually stuck in development. Now as a plus Pikimin serves as a strong launch title that won't over shadow 3D party titles. Even if those 3d party titles are practically no more than slightly enhanced ports simply because the art direction of Pikimin won't compete directly with the same audience.

actually they were going to do it on wii but then moved it to wiiu because of its capabilities

they weren't keeping this a secret at all
in an interview right when it ended they said it was running in the 360/ps3 engine

chipvader here
u may know me, im from the 3ds forums and a few more. im a huge nintendo fan, i plan on getting a 3ds soon and a wii u too