This has always been my thought on the whole, Wii U control input thing.
I think the Wiimote+Nunchuk will be the Classic Controller of this gen, it will be supported for games that might work better with it, but ultimately it will be secondary, Nintendo did show off the Wii U almost strictly as the controller afterall.
I mean look at all the confused people last E3, (even though it was obviously a new console) they were confused because Nintendo was pimping next-gen as "hey look at our new controller, it's got a sub-screen". They weren't even showing off the console, so I would be stunned if after all this that Nintendo is going to then not have the Wii U controller be the primary controller.
Like I said, the Wiimote+Nunchuk combo will be used but for a minimal amount of single-player games like the CC and CCP were, and it will be used for local multi-player as well since Nintendo is about affordability, as well as 4 sub-screens going at once probaly isn't possible. So when it comes down to it almost every single-player game the sub-screen will be the primary controller, not the Wiimote.