I am pretty much picturing there being two teams for LOZ:TP
The Gamecube team is pretty much adding new subquests and small touches to both games.
While the Wii team is working to perfect Wii controls, and anything Wii-specific. I would not be surprised to get a special Wii-specific item, or special mini games that don't exist in the other Twillight Princess.
But I bet NIntendo is really working hard to perfect the control issues with the Wii game. I bet when the game is released that the Nunchuk sword attacks are gone. Those are much better situated for the dodging and rolling away from an attack, in my mind.