Yes, Beedle.  That Beedle.  But before we can even jump into how he relates to any of this, we must travel further back still, to the very opening cutscene of Skyward Sword.  

In this cutscene, we hear a very dumbed-down tale of how Demise invaded the surface world that was ruled over by the Goddess Hylia; to protect the sacred relic placed into her care by the Golden Goddesses, Hylia rends a piece of land from the earth and sends it skyward, leaving the Goddess Sword and the Triforce with it.  Together with the remaining peoples of the Surface, she seals Demise away, and millennia later the events of Skyward Sword transpire.  The entirety of this cutscene is not in and of itself very important, but I would like to draw everyone’s attention to one particular line uttered by the narrator during this sequence:

“To prevent this great power from falling into the hands of the evil swarming the lands… The goddess gathered the surviving humans on an outcropping of earth.”

It is worth noting here that - though the word “Hylian” itself only appears in reference to the shield which bears its name - Skyloft is comprised entirely of people with long ears.  Keeping these things in mind, let’s go back to Beedle.

Beedle is, by all intents and purposes, a fairly unremarkable character in Skyward Sword.  That is to say, outside of providing Link with goods throughout his adventure, he bears no significance on the plot in any capacity, having only a single sidequest that involves retrieving a pet beetle (snickers) of his, for which the player’s reward is a small sum of Gratitude Crystals.  But there is one, throwaway line of completely optional dialogue you can trigger towards the beginning of this sidequest, and it is upon this line that the entire basis for this theory has been built.  When meeting Beedle on his home island apart from Skyloft for the very first time, the player is given the option...

...to comment on his accent.

[after selecting “Your accent!”] “Hmmm? The mellifluous timbre of my voice sounds different to you?

...Perhaps a touch, I suppose... But pray, what does it matter, hmm?”

What’s important to understand about accents is how they come about to begin with: namely, slight differences in pronunciation and rhythm of speech evolve over time as the language (in this case, some form of ancient Hylian) spreads to different locations.  And of course, everyone who uses spoken language has an accent, but Link’s remarking upon Beedle’s is an indication that his pattern of speech is different from his own.  In most other games, this would be unextraordinary - but in the context of Skyward Sword, where humanity has been isolated to a (relatively speaking) small outcropping of earth in the sky, it becomes extremely noteworthy.  No one in Skyloft should have “an accent,” because theirs is a society and culture so small in scale that they should all have the same accent.  Beedle having an accent makes sense if, and only if...

...he’s not from Skyloft.

And if he’s not from Skyloft, the logical conclusion would be that he must be from the Surface.  In almost any other circumstance, this assertion would be smashed to smithereens by the sheer fact that getting to Skyloft without a Loftwing - companions blessed only to those who live in the sky - should be an unattainable feat. And yet, of all the people in Skyloft, Beedle is the only one who could have achieved such a thing... 

...because his shop - which conveniently doubles as his house - is an electricity-powered flying machine.  Within the context of the game, such a contraption seems almost nonsensical; if he were from Skyloft, why would he not just set up shop in a permanent location?  Even if he wanted to live on a smaller island by himself, the people of Skyloft could simply use their Loftwings to reach him (which they still need to do, anyway!).  Indeed, the existence of Beedle’s Shop makes far more sense...if it already existed by the time he arrived there.

Which brings us back to that introductory cutscene.  The narrator states that Hylia gathered up all of the surviving humans (notice the use of the word humans here) onto an outcropping of earth and sent them skyward, and on a surface level, this seems straight-forward enough - but with the revelation that Beedle is very likely from the Surface himself, it’s very obvious that this is nothing more than a bold-faced lie.  Some humans were left behind - they couldn’t all possibly have fit on such a small piece of land - and those humans were the ancestors of Beedle, in some way, shape, or form.  What became of those humans is another matter altogether (one I will address briefly), as the Surface we explore in Skyward Sword is perfectly devoid of human life, barring Impa.

Now, let’s bring it back home: remember how I said that all Skyloftians have long ears?  That was a bit of a white lie, though only if you count Beedle among that number.  In truth, Beedle’s ears are obscured by the bowl cut of his hair - but this is true for every game he appears in, and the general consensus is that they’re round.  This would make Beedle the only round-eared human in the entire game...and he, coincidentally, happens to be from the Surface.

Before I go any further, I’d like to establish a very base reasoning for the existence of long-eared qualities in the human races of Hyrule.  Hylians are far from the only ones to bear long ears, what with the trait also presenting themselves in the likes of the Sheikah and, by the era of Breath of the Wild, even the Gerudo - though it is exceptionally notable that in Ocarina of Time, the Gerudo have round ears, and Ganondorf is no exception...at least, at first.

Y’see, what’s especially notable about Ganondorf is that he is the same exact character is each title he appears in, and in The Wind Waker and Twilight Princess, his ears are long.  This was actually something I only noticed quite recently, upon which I then fervently began scouring for information about his appearance in Ocarina of Time to try and make sense of it all, and the results are...very intriguing, to say the least.  Below is a comparison of Ganondorf pre-timeskip vs. post-timeskip from the original Nintendo 64 version of the game:

As you can see, his model has changed in a number of ways, but... Well, I’m sure you can see where I’m going with this.

Amazingly, his ears got longer, which is...an interesting choice from a design perspective.  Of course, it leads one to wonder why - and far and above the most significant thing to happen to him in the seven years between these two appearances is his procuring of the Triforce of Power from the Sacred Realm, a relic of the old gods.  Evil or no, Ganondorf had forged a bond with a god unlike any had before him, and for some reason, this elongated his ears - so much so that by the time of Twilight Princess and The Wind Waker, they are indistinguishable from your typical Hylian’s.  It is notable, too, that the Sheikah (who have always had long ears) also bear a special connection to the gods, living to serve Hylia and, later, her reincarnation as the princess in the Royal Family of Hyrule.  

“They say we Hylians have big ears in order to hear the voices of the gods.”

So now, keeping everything I’ve talked about here in mind, I think it appropriate to go over the series of events that likely transpired, beginning from Demise’s invasion of the surface world:

In a bid to keep the Triforce out of evil’s grasp, Hylia formulates a plan to send both it and the Goddess Sword out of harm’s way.  She selects - perhaps by chance, perhaps by choice - a not insignificant number of humans to live on this skyward isle, but naturally not all of them can make the cut.  These chosen humans would go on to found Skyloft, a land whose culture revolves heavily around the reverence of the very goddess who saved them and enabled them to live in prosperity (the existence of the Wing Ceremony, the Statue of the Goddess, etc.), while the humans who remained on the surface, left in a world scarred by war and ravaged by monsters, sought new lands, becoming the ancestors of people who would found Holodrum and Labrynna, to name a couple.  In their reverence of Hylia, the people of Skyloft would develop long ears, as even the Sheikah had - but the humans left on the surface world...would not.

That is to say, the Hylians we see in almost every major installment of the series are the direct descendants of the people of Skyloft, and round-eared humans are the descendants of the people Hylia left behind.

Of course, not all humans fled from their homeland - though we see none in-game, it’s important to remember that we also see no Sheikah aside from Impa, though we know they are great in number.  Beedle was, undoubtedly, one of these very few stragglers, and with stories of a land beyond the clouds on his mind - legends that have been passed down over countless generations - he sought to find this paradise by any means, through sheer blood, sweat, and tears (but mostly sweat, if that cycling is any indication) if necessary. In the end, he was successful, and he lives among the people of Skyloft fairly unassumingly - yet he also lives apart from them, on his own island because, at his core, he is not one of them, and never will be.  He doesn’t get all of this Hylia stuff, and frankly, he doesn’t care - so long as he can chill on his own little crop of land with a full belly, a full wallet, and his pet beetle, that’s really all that matters.

And speaking of Hylia - the reason they are called Hylians is because they are the descendants of those chosen by Hylia, even if the knowledge of Hylia’s existence has largely been lost to history by the events of Ocarina of Time and beyond.  (In a very similar vein, it is my belief that Lake Hylia also gets its name from her because the crater that would later become that very lake was formed...when she lifted a gargantuan outcropping of earth into the sky.)   Hylians largely dominate Hyrule for so much of its history because the people of Skyloft were the ones who founded it - yet by the era of Twilight Princess, we see that a great many of the humans who had moved onto different lands have slowly but surely made their way back towards the place they once called home.  

But I would be remiss to neglect to go back to Breath of the Wild; this game is a much more peculiar case, taking place in an era many millennia after any game that came before it, where reverence for Hylia is once again commonplace - so much so that statues bearing her resemblance have been erected in every town, village, and city across the country.  Humans are once again practically nowhere to be seen (except, again, perhaps for Beedle), and even the Gerudo, who have now long intermingled with Hylians for the sake of having children, have inherited the trait (perhaps in part due to the fact that some of their own may worship Hylia, if the statue in Gerudo Town is any indication).  In every single instance, no matter where you turn, these long ears seem to be a direct correlation to the people’s connection to the gods of Hyrule - but rather than their ears being a predetermined factor in how strong this connection may be, it seems that their faith is what influences this trait to rise to the surface, over how ever many generations or centuries that just might take.  (Ganondorf Dragmire, who lives in a castle and inherited a relic of pure godly power, is an outlier and should not be counted.)  As Shad so eloquently states in Twilight Princess:

“Hyrule was made by the Hylians, who, as we all know, are the closest race to the gods.”

And as long as we’re talking about Shad, I’d love to begin wrapping up this post by bringing things round to Twilight Princess once more - specifically the context in which Shad says the above quote, which is far and away one of the most peculiar instances of casual lore-dumping in the entire series.  The quote in its entirety from the North American version of the game reads thusly:

“At the moment I'm absolutely entranced by the sky beings known as the Oocca. Yes, according to legend, Hyrule was made by the Hylians [...] But also according to legend, long ago there was a race even closer to the gods, and some say these creatures made the Hylians. When they created the people of Hylia, they simultaneously created a new capital, a city that floated in the heavens.”

What Shad is saying here is extremely farfetched, particularly for those of us who are familiar with the Oocca.  But in truth, this was a minor mistranslation on Nintendo of America’s part; the original text from the Japanese version of the game clears actually reads much more like this, when translated correctly:

“The common opinion is that Hyrule was created by the Hylia people, the race closest to the gods, but...truth be told, there's also a theory saying that in ancient times, there was a race even closer to the gods than the Hylia people, and THEY created it [Hyrule]. And they, simultaneously with the birth of the Hylia people, created a new capital, a capital that floated in the heavens.”

So the Oocca - the bizarre, Cucco-like creatures who inhabit the City in the Sky - did not create the Hylians, but rather established the kingdom of Hyrule itself in the world that the goddesses created.  But even with this mistranslation squared away, that still sounds incredibly odd, especially taking the events of Skyward Sword into account; we know that the people of Skyloft are the ones who inevitably found Hyrule, because we see the beginnings of this happening at the end of the game.  Funnily enough, it seems that the very line that was mistranslated in the North American version of the game...was the result of mistranslation itself.

In-universe mistranslation, that is.  Millennia of history being told, written, lost, and found, translated again and again and again, until it barely resembles its original state.  What likely happened was that the Oocca, who live in the sky, were wrongly credited with the creation of Hyrule because the Hylian people who would go on the found Hyrule also came from the sky, as they were the people of Skyloft.  Shad’s claim that the Oocca were “a race even closer to the gods" than the Hylians may not be entirely unfounded, however, as it is incredibly likely like the City in the Sky we see in Twilight Princess is what remained of Skyloft after its human inhabitants abandoned it; the Loftwings that the people of Skyloft had for so long relied on would go on to evolve into more sentient beings, suspending the city above the clouds long after Hylia’s magic had worn off - and Loftwings were, as the people of Skyloft believed, beings bestowed upon them as a symbol of the goddess’s divine blessing.  In this sense, it is somewhat true that the City in the Sky and the Hylians were created at the same time; when the Skyloftians abandoned their home to live in a new land where they were not long after christened the Hylians, the skyward isle that they had left behind found a new purpose, and a new “city” was born.

Of course, maybe Shad was off his marbles (even if the Oocca are evolved Loftwings, there is still much about them and their connection to the Sheikah that remains shrouded in mystery), but the crux of this entire narrative is that the people of Hylia, the Hylians - at least, up until Breath of the Wild is concerned - were the descendants of the people of Skyloft, and Beedle’s eccentricities in the context of Skyward Sword are rather convincing pieces of evidence that this did not comprise all people of the formerly-known-as “Land of Hylia.”  It is therefore only natural that a conclusion could be drawn about where the distinction between the two peoples comes from.

But in the end, even if this can answer the question of why there are round-eared humans alongside long-eared ones, it does not answer the ultimate question of what this distinction means.  Why does a connection with and a faith in the gods elongate the ears of the people it touches?  The Zelda Encyclopedia states that “in the past, Hylians were able to wield magic of considerable might,” a trait that could possibly distinguish them from your typical human being - but the canon nature of the Encyclopedia is...shaky*, at best, and downright disrespectful at worst.  Link and Zelda are two Hylians we see wielding abnormal abilities, but their power can be explained with their respective pieces of the Triforce, not to mention the countless magic users in Hyrule and beyond who aren’t Hylian.  Even if there was a time when the Hylians had special abilities, those abilities have long since faded. They are no no taller, no smaller, live no longer than their round-eared counterparts; they are, in every aspect aside from the length of their ears, in every way identical.  To finish the quote by the unnamed Hylian man who speaks to a young Link in the Castle Town Market in Ocarina of Time:

“They say we Hylians have big ears in order to hear the voices of the gods...but I've never heard them!”

So...there you have it.  I must admit that it is entirely possible that the people of Skyloft had developed long ears before their ancestors had been sent to the heavens - after all, the Sealed Temple was, in millennia past, a temple erected in her honor.  Yet this would also make the story of Hylia gathering the “surviving humans” in order to save them all the more grim; could the gods be so callous as to save only those who respect their divine might? One cannot help but think of the Great Sea in The Wind Waker - for in a world populated by the descendants of those who were chosen by the gods to survive the coming floods, it is difficult not to notice that ears of the round variety are once again nowhere to be found.

And yet, when you get right down to it - though some Hylians seem to rely on their lineage as “the closest race to the gods” to maintain an image of self-importance - the difference between a long-eared Hylian and a round-eared human appears to be, ultimately...only that.  And unless we see our round-eared friends return in a potentially future title, and the difference remarked upon, that will likely be how things remain.

Until that time, I will continue to do my best to fill the gaps with which we have been left - even if, at the end of the day, I’ve written nothing more than a meaningless, nine-page word jumble...about ears.

EDIT (5/9/2020): It has been brought to my attention (courtesy of @heartenvy​​) that there is a mild inconsistency with the narrative that Beedle could be from the Surface: namely, the “unbreachable” Cloud Barrier, something Hylia herself created to divide Skyloft from the Surface and keep its inhabitants and the Triforce safe.  However, I would argue that the Cloud Barrier is not a physical barrier so much as it is a mystical one, meant to both keep its location secret (the barrier itself is completely invisible from the Surface) and to ensure the people of Skyloft remain complacent in their isolation (believing Skyloft is all there is, they remain there, and in so doing their long-forgotten secrets are kept safe). Zelda is pulled through it long before any proper portals are actually opened, and I would argue that the portals (that is, the pillars of light that appear when we place the corresponding tablets) are largely a gameplay mechanic meant to keep the story linear, as in a real setting Link would have simply ridden his Loftwing to and from the Surface and would have been able to fly anywhere he chose.  It’s possible the barrier acts to keep out evildoers, specifically (which would explain why Ghirahim had to summon a vortex to pull Zelda through it, where he could reach her), or, not unlike the Isla de Muerta in Pirates of the Caribbean, Skyloft could very well be “an island that cannot be found except by those who already know where it is” - which, to me, makes the narrative of Beedle finding his way there all the more entertaining (the dude must have been, like, super determined).  In any case, I stand by what I’ve stated before: that Beedle is from the Surface, as his accent and the peculiarities of his shop make too strong a case to ignore.

*              *              *              *              *

*The Zelda Encyclopedia states that Termina is a Dream World, despite Link’s Awakening having already done this and in a much more satisfying way.  I can’t take anything it says seriously.