Having Link be a girl would be the most seamless way to create a mainline TLoZ game with a female main character. It would fit perfectly into the lore, require no changes to the core Zelda formula, and aside from Link's gender and the subtle differences that could result in, it would allow for a Zelda game to be created from the ground up in such a way that pretty much completely fulfills fan expectations (get a bow, get this blue tunic to breathe better, be the Hero of Time, etc. etc.).
A game featuring Zelda as the main character would call for significant changes to the formula, in my opinion. If they were to eventually go that route, I'd prefer they go all the way and build a game particularly suited to her character.
Besides, Link has a certain place in gaming culture that Zelda just doesn't. Zelda getting her own game would be a big deal, but I think it would be more impactful to see a female Hero of Time. And it would just make so much sense. Having a female protagonist isn't necessarily my overriding motive here (don't really feel the same way about Mario, for example
), so much as it would be such a missed opportunity not to eventually have a female Link.
Anyway, not trying to fuel the flames of the "should Link be a girl?" debate, especially knowing how fanatical certain people can get over that. Just explaining my version of the "would much prefer female Link to having some other female protagonist" perspective.
Edit: I'm now realizing that I've conflated every Link with the OoT Link by invoking the "Hero of Time" thing. I'm sleepy. You get my point, though.