I honestly believe, like Crow! said, that every contrller has potential except for Wiimote only. For top smashers, again like someone before me mentioned, often don't want to have to retrain their muscle memory, others simply honestly believe the GC controller is the best.
I personally am a Wiimote + Nunchuck user, and I play with that better than I ever did with the GC controller, because I had my mind set on learning to use the Wiichuck set-up.
One advantage of the Wiichuck that may be negligible to most people, but would come in handy in top level play, is the ability to play without having to move any fingers from their locations. It would present differences in only fractions of a second, but in competitive play that could hold an advantage.
The default configuratin is pretty horrible though. My recomendation would be to change the Dpad into smash attacks, using C for jumps. I personally have Up, Left/Right on the Dpad for smashes and Down on the Dpad for jump, because it lets me short hop easily. I don't use Dsmash much so I'll usually just use Shake smash for it.