Hi! I just ran into this myself, and thought I'd post this for anyone else who had this issue to give an alt method, If you want to configure it with the GUI (which may be easier). It takes a few steps, and you will need a mouse.
install Desktop in Raspconfig
2 use the dekstop terminal to run QT_QPA_PLATFORM=xcb /opt/retropie/emulators/dolphin/bin/dolphin-emu
3 configure your controller
4 important- while you are here, configure your hotkeys as well. Dolphin does not recognize the normal hotkey /exit button, it uses its own.
You can edit both GC and Wii controls this way