I think OP could had made a better title for this thread, but I agree with some of his points.
The Wiimote, as a motion-control device, had it's share of problems and doesn't work on all genres, but it was still a control scheme that could had been improved just like the NES controller was improved in the transition to SNES one. But instead of improving the controller and address it's flaws (More buttons with better placement and and other possible improvements), Nintendo goes back to a traditional joystick with it's own improvement (touch screen).
Even if Wiimote comes in the package, it seems that Nintendo didn't even bother to improve anything except maybe motion+. No extra buttons or placement. It feels like Nintendo simply gave up trying to sell motion control for gamers and developers and is leaving it there because of convenience (It's wireless control, easy to link to the console and appeal to retro compatibility).
And now it comes the main problem in my opinion. If Wiimote and Nunchaku does not come packaged on WiiU, then it's a no-brainer that most developers, and I'll include Nintendo ones too, won't even bother with the Wiimote option.
If it does come packaged with the console, then developers will focus their efforts on the UPad as main control scheme. If they make optional control schemes, none of them will fully take advantage of their capabilities because of the other. Hell, In a Online FPS, Wiimote users would completely destroy UPad user. I know there will be games with both options and great schemes and combined implementations, but most won't.
And I'm not going to lie, ZombiU looks like a really awesome game, but mostly because of the concept of the game itself. I didn't think the use of Upad that OMG and I think I would rather play with the Wiimote. And I honestly would be more excited to play Arkham City on WiiU if it supported the Wiimote and Nunchaku.