I still hold a little hope that BotW Link is a newcomer. Link, as a character, is never the same person. Smash 64 to Melee worked, since it was the same Link. Melee to Brawl too, because OoT and TP Link are among the most similar Links, plus they're related. Then comes Smash 4 and Skyward Sword Link is overlooked. SS Link has no boomerang, and he's a trained knight of sorts. His swordsmanship is much more refined compared to OoT and TP Link's wilder style. It made sense to overlook him taking that and Zelda/lack of Ganondorf into consideration.
But now Breath of the Wild comes in, and we know Wild Link is in the game. How will Wild Link fit into Link's previous moveset? His bombs are drastically different, and he lacks a hook/clawshot. Would they change the moveset to reflect those? Or will they just leave the bombs the same and change the clawshot for Magnesis? Among the Zelda characters, Link is the best represented by a big margin. His unrefined sword style has always felt in-character and his kicks help show he is not a swordsman. All items work like they do in the games. Ignoring the big change in bombs and using Magnesis as a grab/a normal grab would be a step back from current Link.
Wild Link is vastly different from OoT/TP Link. Even though he once was a swordsmanship prodigy, he's forgotten how to fight. For most of the game Wild Link scavenges for weapons and uses them as a means to survive until he gets the Master Sword, and even then gameplay forces you to use other weapons. Limiting this Link to just the Master Sword seems a tad unfair compared to how well current Link's moveset has fit his past designs.
Having Wild Link just be a cosmetic replacement would be very different from how Link has been treated. A Wild Link newcomer would also mitigate the issue with Ganondorf not having a matching design. Keeping TP Link, Ganondorf and Zelda like they are, giving Zelda a BotW costume and adding Wild Link as a newcomer seems like the best option for all the characters, unless reworks are happening. I don't think having three Links is an issue, since they would all be different persons. You'd have to be pretty ignorant of the franchise to complain about "Link" taking three spots, and at that point I don't think that person's opinions should matter.
Zelda, on the other hand, has a loosely fitting moveset, and having a BotW design go with it is not as much of a stretch.