The controller on the Wii differs from typical videogame controllers, as the player swings it around in many games, as they would a tennis racket or a sword. This of course makes us wonder if the pain that people are feeling is not injury, but rather the typical soreness associated with actually getting some, you know, exercise.
I can relate to this to a small extent, although I find the Nunchuck controller is far more uncomfortable to hold after a long game session than waving your arm in the air.