Tsk, KDR. The controls are BETTER than GameCube. I absolutely know what you're talking about, I far preferred Wind Waker's controls to the N64 games mostly due to the camera, but aiming and throwing are both much easier on Wii and the camera controls are improved over the N64 games. The sword control isn't technically better, but it's more fun.
But I suppose I shouldn't be making you feel bad! You may still like the Cube version better since I seem to remember you played Wind Waker first of all.