@acris Unfortunately this one wasn't resolved either what I did now which helped with Gamecube at least is to Alt+F4 into dolphin and set up my Xbox Controller which immidiately resolved this issue at least in the Gamecube.
Still trying to figure out the mapping for Wii though. Which is a bit tricky when Dolphin doesnt want to comply with simple mouse clicks. But perhaps this will help you fix this issue. I mean I had to set up the Controller inside of Dolphin perhaps you can automate this.