Hello. I'm using a Switch Pro Ccntroller connected through Bloopair and that can control the RA ui fine.
I haven't tried with a GC controller.
A couple things you can try..
Have you tried setting up a Menu Toggle? (this probably wont fix your issue but its good to do anyway)
Goto Settings
Goto Input
Goto Hotkeys
Then set Menu Toggle (Controller Combo) to something (if your using a GC controller I guess the Hold Start for 2 secs would work well)
Then save your Retroarch.cfg
(Main Menu>Configuration File>Save Current Configuration)
Have you tried setting the Controller you want to use to player 1 once your ingame?
Once ingame open the Menu.
Goto Controls
Goto Port 2 Controls
Set Mapped Port to = 1
Then go back to game and see if your Controller will now control the game
The reason your having the issue is because the WiiU Gamepad always take priority over other Controllers.
Another dirty way of fixing it is to turn off the WiiU Gamepad before opening Retroarch.. easy way to do that is to take the WiiU Gamepad out of range of the Console then then off the WiiU Gamepad lol