I have the same issue too sometimes when I want to play with two friends. Usually spawning Alt+F5, Alt+F6 and Alt+F7 to connect and disconnect the "Wiimotes" helps.
Haven't found any other way to fix it. Usually when we want to play New Super Mario Bros. Wii it can take 5 minutes before every controller is active, sometimes I have to restart the emulator altogether.
Haven't found any other way to fix it. Usually when we want to play New Super Mario Bros. Wii it can take 5 minutes before every controller is active, sometimes I have to restart the emulator altogether.