If you can get the PS2 version instead, go for it. There are some occasional hiccups using the joystick to draw circles (tip: make sure you actually close the circle), but in general, it works well.
More importantly, on the PS2, the attack function is assigned to one of the regular controller buttons. On the Wii, it’s assigned to shaking the controller. This difference is quite significant, especially when you start doing multi-hit combos on monsters. It was enough of an issue that my girlfriend happily abandoned a few hours of progress in the game in order to play the PS2 version, once I showed it to her. Thank goodness the Wii copy was only a rental.
Anyway, if you’re at the Kohana Shuffle, you’re really just getting started. It’s worth switching now rather than trying to power through another 40 hours of shitty controls.