I used to play with the GC controller too, but changed around some more and finally settled on wiimote/nunchuk which I agree is the best choice, ultimately.
GC controller feels great initially, but it's really awkward to jump while boosting, which comes in handy when you're going for time attack on Aquarium Park and wanna run on water/jump. It's also the worst one to do the sidestepping during quick step sections. The surface on the stick coupled with the "heavier" feel makes it extra clunky.
Sideways wiimote I found to be completely useless because there's no real 3D movement and using the B button to slide is super weird, especially if you use the stomp move a lot in conjunction with other moves, which is what I like to do. Movement during 2D platforming is probably the best with the dpad, but I don't find the tradeoff worth it.
Nunchuk and Wiimote combo has every button readily available with one finger on each at all times, making for the most fluid playstyle. The analogue stick on the nunchuk feels nicely loose and seems best calibrated to deal with the sidestep stuff, even though they probably remain the weakest part of the game. The only slight issue with this control style is that you need to shake the wiimote more than you'd prefer to get wisps to trigger, but this is the same issue as sideways wiimote, and when you get the right whip motion going, it's mostly alright. By the time you need split second timing on it you know the level so well that you come prepared though.
It continues to be a rediculously fun and addictive game. I've made feeble attempts to play Assassin's Creed Brotherhood, but keep somehow ending up playing this instead.
