A game with both of them would be interesting but seems like a considerably more difficult concept to pull off so I'm not so sure they'd go that route.
...How? Literally nothing changes. All Nintendo has to do is allow you to pick your gender when you pick your name. Sure they could have a proper character customization thing, but having any changes to the story would be completely optional depending on how it is written (for example: in Twilight princess Telma's flirting will work though a little scandalous, but the scene where Link and Mayor Bo share knowing glances while Ilia yells at them would work better if the mayor and Ilia's genders were reversed). But literally 95% of all Zelda games' stories work just as well as is if you pretend Link was female.
Maybe you can have a story where Link and Linkle are fraternal twins and the one you choose becomes the hero while the other takes on NPC roles throughout the story. (Imagine a conversation between Link and Linkle)




