I'll probably try the Wii + Nunchuck, but I will be using the Gamecube Controllers most of the time since I am used to them.

its look like many people would still be playing with their gamecube controller

Wiimote + Nunchuk. I want to try something different :)

A) Wiimotes or Wiimotes+nunchuck DO NOT use motion control, so don't be afraid to use these setups. They're just as much "for a fighter game" as the other 2 controllers.

B) Flicking the right stick on the GC or Classic controller does nothing if I remember correctly, unlike in Melee where it does Smash attacks.

Nunchuk, then GameCube

I will certainly give the Wii-mote/chuk a go. Checking players in Mario strikers had a very satisfying feel to it, so hopefully the manage to capture a similar feeling.

If it sucks i'll head back to the GC controller.

GameCube controller. Since I only have two of those I’ll probably mix it up though.

wiimote/chuk

it should be the same as gamecube for normal play but then hopefully u can point at the screen for using the final smash attack on those that have u shoot missiles

Most likely wiimote/nunchuck, because I'll be able to separate them.

@fastrabbit

you can't use motion sensing with the wiimote in SSBB