Legend of Zelda is not an RPG, Link is not YOU, he is Link, an established character with an established history. Certain parts of his appearance are just part of his character, the overall tunic design of his clothes for instance. In TP even his eye-color had explicit story significance. His appearance is the way it is for a reason.
I don't think being able to customize Link will do anything for the game, if anything it would make me feel disconnected from the world of the games if his appearance was drastically different. The different armors/tunic colors already used in previous games is enough I think.