I think the Puppet Ganon fight is meant to represent something very important about Ganon as a character. Not only is it a showcase of his magic, and his constant desire to challenge others for amusement, but also shows his desperation. This desperation to kill, to inflict pain on anyone who tries to stop him is shown from the beginning in Ocarina of Time and continues into Wind Waker.

Easily one of the best Zelda themes of all time

Subarashi