I got the same issue with my wiiu a couple of years back
see what I did on mine to fix it
1. load mocha CFW
2. load homebrew channel with gamepad support
3. exit HBC with gamepad support.
4. load mocha CFW 2nd time
5. load Gamecube injectiin
there is a homebrew channel inject that when you launch it,,it has gamepad support somewhere in the web..
so that when you exit and load mocha then load gamecube it has a controller support.
not sure whats happening to the wiiu when launching gamecube inject..i heard that its a common to other wiiu's and others has wii u load fine