Heck, they could patch her into Wind Waker HD as an optional replacement for Link's sister, where she dons the hero's clothes and "Link" is the one whose kidnapping sets off the plot instead. Plenty of ways to make everyone happy, really.
If they decide to put her into a canon main game, they could always handle it like, say Costume Quest did: Whichever one you pick becomes the main character, with the other being the secondary. The series' timeline could merely mention "the hylian hero in green" and not specify gender or name.
Jo, if anime reverse harems have taught me anything, it's more likely that Linkle would be constantly running into a handsome, muscular Ganondorf on her quest to rescue an gorgeously effeminate, but still male Zelda. That's just how it works when the main character is a girl.
You know, Ganon never has this problem. You know why? Because that is 100% man right there. Seriously, the calf muscles he must have. Mmph. Kinda feel bad for the Gerudo that their only male decided that being literally the only suitor for an entire race of women wasn't as fun as being a pig wizard.
Now, Female Ganondorf is something i could really "get behind"....¬w¬
And the Gerudo tribe flavor-thing? Reverse all the tribe, and problem solved. You just can't think of it because turning a 99.9% female race male feels like new levels of blasphemy...
I always wanted this idea that the hero of time could reincarnate as a hero in green, but did not have to be a male all the time. Linkle and Zelda could just be good friends where then a great evil kidnaps Zelda and you, Linkle, must save your best friend from this mysterious enemy.
Oh wow
When I was reading the page it cutout out in the middle right under the Eer and the Cut the Feed so I thought the page literally cut out in the middle.
Linkle has braids? Mystery solved.
As for gender-swapped versions of other characters, the Direct said Linkle isn't actually Link, just someone who looks similar. Even if she were, that doesn't mean anything for other characters. There's a very story-important reason for Ganondorf being male.