This is exactly why I like the wiimote nunchuk too. Also my cat can sit on my lap while i play and isnt sitting on my arms or i dont lay my arms on her. Its much more comfortable for us both.

nunchuk, gamecube feels awkward for some reason.

I use to be in the exact same spot you're in kazadoom.
SSBB is also my first Super smash game.
I also preferred the wiimote sideways a week ago, simply because I liked the D-pad controls more. But once you get competitive in the online multiplayer, thats when the wiimote's weakness' becomes apparent.
It doesn't have enough buttons.
You can't press up without jumping, the blocking and grabbing buttons are awkwardly positioned, and you have to press two buttons to perform smash attacks. Those are major handicaps.
Right now I use a third party wireless gamecube controller.

I stick to the Wii mote + Classic controller. While the GC controller was pretty sweet, I got accustomed to the classic fairly quickly, made me nostalgic for the SNES days.....if the SNES had dual analogs.

I tried Wiimote, and Wiimote+Nunchuk, and even customized them, but neither felt right after 7 years of Melee...
So the gamecube controllers are the only true way I can play the game. I haven't bothered hooking up the CC, but I don't think it would work for me either...

Wiimote and Nunchuck also.

I've used 2 controllers: Gamecube, and Nunchuk. Gamecube is what I use mostly, since a) I'm used to it from Melee and owning a gamecube for 5 years and b) it doesn't waste my batteries (even though I have rechargeable). The Nunchuk is very comfortable though...it's nice to keep your hands as far apart as you want.

I have been using the wiimote, wiimote + nunchuck and the gamecube controller and my best choice is the Gamecube controller, it feels right playing it with the gamecube controller and weird with the wiimote and nunchuck. but I can't say much about the classic controller since I have never owned one before

Classic controller. And I refuse to try any other methods.

Wavebird all the way! Best controller created... ever.

I also tried the Wii mote sideways and Wii mote and nun chuk. Dont have a classic controller yet. IMO the Wii mote sideways is garbage.