I found on super mario world for snes.
With gamecube controll that the run button is very inconviniently placed.
the jump button is B and run is X so you have to hold the control wierdly to run and jump. I cant say for Classic control as i dont have one. one ,more thing i have to add is i dont understand why you cant use wiimote to play it as there is more than enough buttons and there would be a few good layouts for it. (i just guess its a way for nintendo to make us payout for gamecube or classic controlls)
one other thing is it would be better to let us choose our buttons like control configuration.