I cannot imagine not using the GameCube's controller. Let's piece this apart...
Remote: There is no way a D-Pad could offer the precision I need, there's no C-stick (I use the C-stick FAR more often than the A button), no equivalent for X to jump, I am used to using R to shield, etc.
Remote + Nunchuk: No. I'd use B for shielding, A for A-attacks, and already I have nowhere to go for special attacks and no potential jump button.
Classic Controller: Hmaah. I don't have one, but isn't the D-Pad where the control stick should be?