Well if you think about it, you can't really compare these to games because one is an adventure game while the other is a music type of game. They are just too different. But, if I had to choose it would definatly be Twlight Princess because I'm a huge fan of Zelda games, and I love Link.
i say that GH3 is just another music game....i find it kinda sux. i definately prefer twilight or GH3 because well its an adventure game and its fun. (heh shooting goblins off their boars)its kinda difficult to compare the two because one is an adventure puzzle game while the other is music and rythem game