Pro Controller.
Because: No wires, motion controls, rumble, is more beautiful, and NO WIRES.
I don't see how the GC controller could be better because the layout it has. Smash barely uses half of the buttons of any of these controllers. It has a lot of repetition on the buttons, like.. In the default control scheme, we have two options to grab, shield and jump, and the right analog stick is just like a shortcut for the smash attacks that you can do with the left analog stick and the attack button...
So, the layout of the controller is not really important, for example, I dont see how the A button being on the center of the GC controller and being so big helps anything, even because it not necessarily the most important attack button to me, I really use the attack and Special Attack in a very balanced way and depending on the character... So.. this layout doesnt help anything to me and I actually preffer the most simetric style of the pro controller, that has the standard shape of any recent joystick. I think I dont need to pretend that the gameplay of smash is so special that there's a need for a specific controller only for this game.
You can configure any controller the way you want. Unless you wanna adapt to a new shape of controller just to play Smash, I dont see any reason to try to get into the GC Controller.