I'm miserably sick and can't sleep, so fuck it, have a probably rambling essay on why Wind Waker's Master Sword is fake, adult timeline Hyrule probably practiced eugenics both pre- and post flood and the kokiri are genderless master shapeshifters.
Warning: this will debate uncomfortable topics.
I'm going to start with the Mastersword. The basis for this might sound a bit familiar if you watch Zelda theory videos, since that's where I got introduced to the idea, but I think I've come up with a defense that's mostly my own at this point.
Let's start with the basics. We learn in Skyward Sword that the Mastersword was mostly man-made, more specifically that it needed a person and sacred energy to infuse an already holy blade with enough power to become the Mastersword. We learn in Minish Cap that Hyrule has other holy swords and other sacred energies, in particular in the Royal family of Hyrule. So, it's already theoretically possible.
Why can't it be the real one? Well. A truly sacred object cannot lose its status without an actual act of desecration. Think how a church a violent crime happened in needs to be sanctified again before being acknowledged as holy grounds again. Yet the Mastersword in Wind Waker has somehow lost its power enough to need constant prayer from two saints - sages - for maintenance. We know this isn't a natural act because Twilight Princess's sword simply... doesn't need that, so it can't be due to simply time. And we know it can't need it because Ganondorf didn't target them, despite targeting the descendants of the sage that he killed, likely so that person couldn't be replaced - he killed Rutela and was hunting her son, and the missing sage is the water one. If the sword already needed the constant prayers, that needs sages that aren't immortal because they're not in the sacred realm. If they're not immortal, they'd need to be replaced, and then it would become known that hey, there's sages that keep the legendary Mastersword empowered. Not to mention the Kokiri, who are needed for one of the temples, aren't even around anymore.
So we can safely say that, at the very least, something happened to the Mastersword between OoT and WW. Why does that make me think it's fake?
Because A Link to the Past doesn't need them either.
Why is that important? Simple. This is a timeline where OoT Link was murdered with the sword in hand. That's true whether you think he was killed in the final fight against Ganon or because the sword didn't seal him and tiny nine year old Link immediately stumbled upon angry foiled Ganondorf. In either case, this ought to be the most desecrating thing that could ever happen to that blade. Remember, that's still Fi, specifically made to guide and keep safe Hylia's chosen hero, Link's very soul, against any form of Demise like, say, his literal hatred incarnate. Not only would this foil its/her literal sacred purpose, there is every chance that the sword also got stained with his blood. Which means blood of a literal goddess chosen hero, martyr and possibly sort-of demigod depending on how you interpret growing up among immortal spirits and then being sealed in the actual sacred realm to alter one's very essence, is very possibly on that blade, which is incredibly desecrating.
And the sword still works just fine.
Yes, you might argue we just don't see those sages and all, but consider this: here, not only are there no Kokiri, the Zoras are, safe for a few exceptions, actively hostile to the Hylians. How well would asking them to man a temple far from water for the hylian hero go, you think? And yes, they might have asked other races to participate or used Hylians - but we know precisely where all the descendants of all sages from OoT are - the seven maidens - so if, it would have to be new sages, and Aghanim would, as chief advisor to the throne, definitely know about them, so it is very unlikely. Yes, it can be made more powerful, but that has little to do with the sacred status of the blade itself.
So. The greatest possible desecration wasn't enough to weaken the sword, yet in WW, it us so weak as to require constant maintenance. So what happened, that makes me think it isn't actually the same sword?
Well, to put it simply, Princess Zelda happened. See, in the downfall timeline, there is definitely a Mastersword - Link likely had it in hand as he died. There us also one in the Child timeline - we see that one at the end if OoT. But the only point from sealing him on up until the end of the game, the only Mastersword we see in the adult timeline is the one literally strapped to Link's back - the one send back with him, that of the new child timeline. So in the adult timeline, the Mastersword was gone, safe for when Link was actively there, from the moment of the sealing on.
This is also helped by the differences, likely externally caused by the different stylistic choices, between WW and OoT and Skyward Sword's swords. WW's sword is comparatively small - Link here is young, twelve years old, and often about half the size of the adults. Yet the sword isn't comically large in his hands. But the sword of OoT would be - the blade was about the same size as young Link after all! Furthermore, the pommel is much larger, and the gem is teardrop shaped instead of a diamond.
But even with both prayers, it's much weaker than OoT's sword. In OoT, it can control Time Itself as well as access to the sacred realm, while in Wind Waker it... just about manages to freeze about half of Hyrule in time. And not even well, the Japanese text makes clear it couldn't even properly seal Ganondorf's magic, just his minions. Like, say, someone knew vaguely that the blade had some sort of power over time, but not anything more precise or how it worked.
Like they couldn't just check the blade itself.
So. Wind Waker's Mastersword is likely a replica. But why, and how did I get from there to the other topics?
Well. The Hero of Time was the fourth legendary hero in the history of Hyrule, fifth if you count the offscreen hero of men. Which means the Royal family, keeper of its histories, descendants of the mortal embodiment of Hylia... probably actually know about the curse of Demise. So in other words, they did not know about timelines, probably, but dud know that:
A) there would be a new threat in a couple of centuries
B) they would need a hero to combat said threat
C) that hero would need a sacred weapon
And D) people would have quite some questions if it were anything but the Mastersword.
So they needed a Mastersword and they needed a hero eventually. The sword they could probably take care of - take a different sacred blade and reforge it and temper it with constant prayer enough to be at least passable - but how to get a hero? Well, they could make a trial - the tower of babel the gods is explicitly one - but a trial still needs someone to go through with it.
The downfall timeline at some point - I honestly don't remember which game it was in - states that any hero must be a descendant of the Knights of Hyrule. Which Knights of Hyrule? Unclear. However, there are a few hints we can follow:
A) must have been from before the Downfall timeline, as it's the reason ALttP Link and his uncle were the ones contacted by Zelda
B) a clear, definable group, that aren't just the castle guards - this is easily proven by Impa not even bothering with them in the original Zelda but heading out to search for a hero instead. So, one clearly defined group that cannot simply be joined it must be.
C) defined and likely lived after the events of Skyward Sword, as previously there was no place called Hyrule.
There is an easy answer to who that group may be, and it even ties in with Demise's wrath: the Knights of Skyloft, a group Link, Groose and arguably Zelda were all part of to different degrees, all of whom aided in his downfall. At least Ghirahim would also be at least aware of them, given he knew where and when to intervene in the Sky, and since Fi can speak telepathically to Link, he might have informed his master of them. Thus, while we do not see it in-game, he might have cursed them too, and similar to how his curse means Link will almost always be there to defeat evil, this one might have tied into it with causing Link to always be reborn as descendant of one of them.
So, assuming they knew who was and wasn't a descendant. How might they have used it to ensure a hero?
This is where we get into eugenics, for those uncomfortable with it. You can skip until the green text, if you want.
Well, the bloodline can't exactly dilute if the only criteria is that it's a descendant. Given there's still heroes these many millenia later, we can assume that fact to be true. So the answer is simple: by making sure there are as many people as possible who have that bloodline, while also making sure they do not intermarry closely enough to cause potentially weakening genetic disorders. Hyrule would have known of the possibility of those, since it was common knowledge even in the middle ages that if you breed any livestock too closely, you get 'abominations'. Hyrule has domesticated chickens, cows, horses, cats and dogs, so they should have that knowledge. Not counting the goats or pigs as they're either later or in a different timeline.
I honestly dread to know how many kids failed those tests in the tower once Ganon returned. The number is probably far too high, and it wouldn't be gentle to them either.
Then the flood happened and it became all irrelevant anyway, right? Well, not really.
See, the problem with WW is that realistically speaking, all of the populations are under the threshold of a minimum viable population with consideration of genetic stochasticy.
That's a lot of scientific terms. What does it mean?
Well, simply speaking: they're all going to inbreed themselves out of existence like the Habsburgers. There are maybe a dozen Gorons, less than a hundred hylians and sixteen visible Rito, only one of whom capable of bearing children, whom Link snatched away from there. Give it a few generations, and unless they have some giant cities hidden away somewhere, both the Rito and the Gorons will be gone. They simply don't have the genetic diversity to survive. And while the Gorons at least managed to cling on all the way to Spirit Tracks, there is no trace of the Rito left.
(I'm ignoring Phantom Hourglass for reason of it's literally a dreamworld and thus not evidence)
But the Hylians recovered. How so?
Well. By carefully managing who had children with whom, most likely. Scientists already did this with cheetahs, which is the reason they aren't extinct, but also why you can take any two cheetahs and swap their organs and their bodies won't even notice it's not their own. This is not as much of a hyperbole as you might think.
But that won't work if they don't know who is related how closely. So, in other words, WW's people, in order to recover as they did by Spirit Tracks, must still actively be practicing eugenics to prevent inbreeding. Likely they also send people from one island to another if they're too closely related to everyone else there, and also likely cannot afford the genetic diversity loss of people staying biologically childless.
Sorry, Maggie. Extremely sorry, whichever poor woman gets paired up with Tingle, providing they don't see him as one of said abominations. That one of his brothers made the tower as a mere child unfortunately speaks against it.
So. How does that relate to the Kokiri?
Those who read the previous section might have noticed I did not mention the Koroks in regards to the minimum viable population threshold. This is because the game heavily implies them to be the exact Kokiri of OoT.
Don't believe me? The Koroks outright say they only recently left their old home in the Lost Woods. Not in one sentence, but two: that you might find their old homes there and that the Lost Woods recently took over. Said old home is perfectly identical to the OoT village. Which means they are at the very least the Kokiri.
Why the same ones? Well. First of all, let's do a quick headcount. In Wind Waker: Aldo, Drona, Hollo, Elma, Irch, Linder, Makar, Oakin, Olivio, Rown, and arguably Fado. That's eleven.
In Oot, discounting Link and Saria for obvious reasons: Mido, Fado, the three Know-it-all brothers, the twins, the shopkeep, the two girls in and on the shop and the three male kokiri outside identical to the know-it-all brothers. Note that at no other instance in the game does a person exist in two places at once. So, despite looking identical, we can reasonably assume them to be different people. That brings us up to thirteen Kokiri.
Given the upheaval, it is not unreasonable to assume that some time during the several centuries between OoT and WW, two might have been lost. Ganondorf, at the least, would likely have struck at a being so reminiscent of young Link, he must've thought it to be either the hero reborn or a relative, and as the drowned of Hyrule can attest, the rains the gods sent didn't much care whom they killed either.
Additionally, the Kokiri - and the koroks, to a lesser degree - are both described as the immortal children of the forest, never growing up and all. The key part here is that it's never growing up, not never changing, as well as immortal in the sense of being ageless. If they do not age, we should be reasonably able to assume we meet at least one of the Kokiri even centuries later - given they were safe enough to live in these same homes until recently, at least one should have survived. So why don't we?
Because the koroks didn't come about through evolution but transformation magic. We know the woods are capable of it - skullkid proves it. A being, a child, formerly of flesh and bone transformed into a living wooden creature and robbed of their memories in the process.
But the Koroks remember some things. And in Zelda, being connected to one type of otherwise harmful magic shields you from the effects of it, at least to a point - Ganondorf, unable to be killed by the blessed sword of a sage, Midna so unaffected by Zant's shadow magic despite being admittedly a less powerful sorceress he only managed to make her an imp through Ganondorf, the Zora and their water magic unharmed by being frozen over and over where any other living being would have its cell walls in pieces - but the magic of the lost woods is explicitely not the magic of the Deku Tree. So, in order to be less affected, it must be the same kind of magic - transformation magic.
In a people that can live forever and change their shapes to the very base level of how their cells are structured - plants versus meat - how likely is it that in a few centuries there have been two beings of the same stature, the exact same hair colour and a strength in the magic associated with the forest (forest temple is a wind temple, after all) of the same name?
(Side note, at least one guide claims WW Fado was a personal friend of OoT Link. Given he obviously never returned to Kokiri Forest, that'd basically force them to be the same, but I'm not counting it. Even if it's the official Prima book.)
Now, the Koroks all have new names, but Fado never changed into a Korok - only a boy. We can still assume that they are probably the same, given there is no interaction indicating any one or more of them to be older than the others. So while the names might be excused as extra layer of disguise, what of the gender change? Especially since Makar, whom we thus must assume knew Fado beforehand, never remarks upon it?
Well, maybe he didn't mention it because to him, there is nothing to mention. In a shapeshifting people of eternal childhood, where everyone plays just the same in the forest, what meaning does gender even have?
And on an entirely different note, Makar, who is possibly Mido as the only Kokiri who even mentioned music at all, had to have had an existential horror of a day when the amnesiac reincarnation of his dead former bullying victim came to pick him up to replace the ghost of a dead friend of theirs in a position with the same title as Saria's.
