The franchise director has explained the choices that led to Zelda's appearance as a playable character in Spirit Tracks

Eiji Aonuma told games™ why the development team finally decided to include the Princess as a playable character in the series. Explaining that they had the idea to include the Phantom character in a quest after solid feedback from The Phantom Hourglass' battle mode.
 
"Why would an archenemy like the Phantom become your ally, we asked ourselves," explained Aonuma. "And during that discussion we came up with the idea that one way would be if a second character took control of that Phantom for you. But who? We thought Zelda might be an interesting and appropriate character."

"So that’s how we decided upon the story where Zelda is going to have her body taken away by an enemy. One of the most important facets of the story would be for Link to regain her body but, at the same time, her spirit form can take on the adventure together with Link." The Zelda director added that the game's producer also saw it as a chance to help clearly identify Zelda's character, which in the past was heavily based on the classic damsel-in-distress, but has expanded in recent games.