I know, you're good, and technically, Spirit Tracks' main focus is actually being able to switch between Zelda and Link in a sense, but having her as the main protagonist is something else. So that's already been done. Unless you mean like the Chapter epilogues from Paper Mario where you control Peach at the end of every Chapter. But even if Link captured by Ganondorf. He's proven countless times that he can break out of any Hyrule prison, Gerudo Fortress if you get spotted in Ocarina of Time, Hyrule Castle, towards the beginning of Twilight Princess. Breaking out Zelda, at the beginning of A Link to the Past, Pirate's Hideout in Majora's Mask, Forsaken Fortress in Wind Waker. Thing is, Link is an expert Escape Artist, if he was to move around a Gerudo Hideout like Peach is able to in Paper Mario. Link's capture will only last 5 minutes at most, and that's only if Link is taking his sweet ass time in the dungeon.