The switch in plot position of Zelda and Ganondorf makes a lot of sense in this story: Zelda used the wisdom she gained from her Triforce piece to amass great amounts of magical and political power. Ganondorf, meanwhile, found that the power he had from his Triforce piece wasn't enough to save his people, and thus gained wisdom. So even though they haven't switched Triforce pieces, they've gained a measure of what the other is generally noted for.
Spoiler for both this story and The Legend of Zelda: A Link Between Worlds: It turns out that the Triforce is kinda important for the, you know, continued existence of the world. Thanks Link, for consigning Hyrule to a lingering death.
