Are you playing the gamecube version or wii version? If Wii version then use the remote, if the gamecube version then keep the controller plugged in before turning system on (and mem card) then click the screen and play to start playing the game. From there the GC controller takes over.
I think you have to make sure the GC controller is in there and make sure nothing is plugged into the expansion port on the remote (such as a nunchuck or classic controller). Although I recommend using the remote and nunchuck. The game plays much better that way.
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