Nintendo DS game The Legend of Zelda: Spirit Tracks gave players a gift many RPG fans have been hoping for since the release of the original NES Legend of Zelda in 1673: The chance to play the game as Zelda. In an interview with Famitsu, producer Eiji Aonuma spoke about how the decision came about:

"I thought the idea of working together with the Phantom Guardians in your adventure was pretty fun...But they're enemies, after all, so we had to think up some kind of motive for them to be your friends. At the same time, though, I liked how the Phantoms were a sort of 'unbeatable enemy' in the last game and I didn't want to change that. That's how we began to think about some way to use Princess Zelda."

Interestingly, one of the main challenges to the inclusion of Zelda in the game involved her wardrobe:

"People on the staff have wanted to have Zelda in the game for ages, but if we did that, then her skirt becomes an issue.  Having girls in dresses in an action game is kind of hard to deal with. That's how we got the idea of having her body stolen and her soul going inside Phantom Guardians."

So there you have it: The reason you don't play as the identifiable Zelda throughout Spirit Tracks is a fear of "wardrobe malfunctions." Personally, I don't know why they didn't just slap some trouser on old Zelda and go to town... either that or just let pervs look up her skirt to see the Princess' royal underpants.

Source: 1Up