I've got Dolphin 3.0 for mac OS X. ive just started legend of zelda wind waker and it works fine. the wii remote i have connects fine as well. but the thing is that after it does connect, none of the buttons work during the game despite the blue light and dolphin saying im connected to it. i turned the gamecube controls off and it still did not work. eventually i found out i had to configure the wii mote but i got greeted with a very confusing screen. i tried playing around with it, expecting some change, but nothing at all. then i realized that the "configure" button says "emulated wii remote" even though on top i selected "real wii remote" as the input source. im actually planning on using my classic controller, but i cannot even get this wii remote thing right. Sorry that this may be very simple..... but no other answers have really worked so far.
