I'd much rather play as Zelda or Link's sister in a world where Link is still reincarnated, but something happened to him. Wouldn't that be so much more interesting than just having a gender swap for one of gaming's most popular icons? Reincarnation or not, for me Link is very much an established character with certain traits I don't want to be changed. As soon as you bring in customisation, it's your character and not Link anymore. This isn't like something like Mass Effect with Commander Shepard either, where it's an IP that was only introduced last generation with customisation right from the start. Here, we're talking about meddling with the face of one of the most legendary and long-running franchises in gaming.
Not to mention, if Nintendo were to do this only once, it would be an expected feature in any future Zelda games. Trust me on that. I realise this doesn't seem to be a popular opinion, but that's just how I feel as a long-time fan of the franchise. I welcome a lot of changes Nintendo has in store for The Legend of Zelda, but this wouldn't be one.