It is simple really. Though any one can mess up even simple things 
Post your settings as screenshots. Click the Wiimote icon (take one screenshot of this) and click the Config icon and go into Gamecube tab (another screenshot of this) and lastly click the GCPad icon for the last screenshot).
Personally, I've never had an issue with any Wii game that uses the GC Controller. Other people have had similar issues, but most (if not all) were issues of oversight in regards to one little setting or another. That's probably your case (if not, then something is screwed up :p).
Post your settings as screenshots. Click the Wiimote icon (take one screenshot of this) and click the Config icon and go into Gamecube tab (another screenshot of this) and lastly click the GCPad icon for the last screenshot).
Personally, I've never had an issue with any Wii game that uses the GC Controller. Other people have had similar issues, but most (if not all) were issues of oversight in regards to one little setting or another. That's probably your case (if not, then something is screwed up :p).