You ever notice how quirklessness shouldn't exist in My Hero Academia. It doesnt add anything to the story. if you gave izuku a quirk that allowed him to change the colour of his hair or alter the number of freckles he has on his face, nothing in the story would chang.
Him being ostracised wasn't because of him being quirkless but because he was seen as a creepy otaku who kept personal notes on other people's biology.
People telling him he can't be a hero despite his dreams could just as easily stem from him having an extremely mundane quirk.
Other than Izuku no other characters seemingly faced any problems from being quirkless. Mirio was still extremely capable when he lost his quirk and was still able to continue on at UA without losing his status as one of the big 3. Melissa Shield didn't face any issues because of her quirklessness.
the worst thing to happen was to Pixie-Bob and that was the Wild Wild Pussy Cats decline in the rankings because they, objectively speaking, couldn't perform to the same standard as before.
The MLF aren't anti qurikless so much as they are anti weakness, wanting to be able to freely use their quirks with some kind of Might makes Right mentality.
Quirklessness only serves the purpose of making Izuku an underdog and that could be easily replicated with a mundane quirk. There is the whole only quirkless people can weird OFA thing now but that has been retroactively added to explain why the quirk isn't being given to someone else.
In a world that values quirks above all else being Quirkless should be a massive deal. Quirklessness should have a huge focus in my hero academia just from implication alone that 20% of the population is "biologically inferior" to 80% even if that inferiority in most cases is extremely negligible, but preceived biological superiority over meaningless differences has caused devastating wars in real life.
Melissa Sheild, despite who her father is, despite the quality of her work, she should face issues for being quirkless in a field that doesn't require a quirk at all, her work seen as somehow inferior with her needing to put in twice the effort for half the exposure.
Mirio and pixie-bob should have been blindsided by their newfound treatment for being quirkless.
But quirklessness doesn't really matter in canon MHA it's only there to showcase a Zero to Hero story with the main character.
20% of the entire world's population is quirkless, if its the same number as our own (low-balling cause its 200 years in the future not the present) at 8 billion then there is roughly 1.6 billion naturally quirkless people in the world. An absolutely massive demographic of people.
Yet there is only 4 quirkless people in the show, with 2 being made quirkless via special bullet or had their quirk stoled by AFO.
I genuinely believe that the concept of people being quirkless is so meaningless that it actually hurts the story and that the show, as it is presented in canon would be better if 100% of the population has quirks.
TLDR: Nothing is done with quirklessness. It's redundant, underutilised and meaningless. Anything quirklessness truly does for the story can be replicated by mundane quirks. I have no idea why the concept of quirklessness isn't explored and wonder why the author wrote about it at all.
Hmm. Beyond wanting to defend early Izuku, there's two ways to look at this: Quirklessness form a lore perspective, and as a story element.
The thing is that, lore-wise? Quirkless makes sense as a thing. Quirks are, what, only a couple hundred years old? Not only that, but the way that they escalated both in power, and commonality? If I had to guess, Quirks probably became 'common' maybe... a hundred years ago, and then things escalated to now, where Quirks are the standard. There's a place within the foundation of the setting itself for there to be a small population of people who are 'normal' in a world of abnormals.
Beyond that, I saw this in a fanfic somewhere and I haven't forgotten this concept: 20% is for the population as a whole. But, if you were to break it down by ages? Quirkless, in all likelihood, is an 'affliction' of the old, because Quirks are always more plentiful and powerful in each newer generation. The reason why we see all of three Quirkless people in story (beyond Hori laziness) is that, in all honesty? Izuku, Aoyama and Melissa are probably the last of a dying breed; within a generation or two, max, I'd expect will be no more Quirkless people born (you know, if the Quirk SIngularity, as in one or two stupidly powerful beings, don't accidently the human race, or people broadly become so powerful to the point where they become ungovernable and society collapses (or if, as some people theorize, Hori just doesn't axe Quirks somehow at the end of the story)).
Tying this back into Izuku? Well, first off, 'Izuku the creepy otaku' fanon really isn't a thing. The, at times infamous, notebook? It's called 'For My Future, Hero Analysis'. Bakugou is offended by it, and burns it, because their a sign of Izuku's ambition to be a hero, which he hates because he loathes Izuku. There's nothing there about... like, his classmates, as far as we can tell, there's just the idea of Izuku even vaguely possibly going near heroics, which would besmirching Bakugou's 'origin story', and thus it must be put down. That's what offended him, and no one else even cared about it.
(And, while I'm on the topic of this kind of fanon, even if you didn't actually bring it up: Izuku the stalker, or Izuku following around Bakugou is also bullshit. When they were little, little kids they were kind of sort of friends, and Izuku followed him then, as part of a group, but after the Quirks came in Bakugou turned on Izuku. Every time we've seen them since he was, what, five? Izuku is avoiding Bakugou, to the best of his abilities, which is complicated by them being in the same class. When they were in the same area he was always cringing, ducking, curling up, all defensive behaviors, because Izuku doesn't want to follow Bakugou, he's afraid of him, and for good reason.
Until well into their time in UA, Bakugou is the only one to initiate any sort of interact with Izuku, and Izuku only responses to him.)
Like, I'm looking at Chapter One right now: the reason all the kids are bullying him? Beyond Bakugou, the most popular kid in school with the same energy as the game winning quarterback the faculty panders to, actively bullying him and everyone following the leader? Izuku is weak, helpless to resist Bakugou's words (which are backed by technically illegal force, as they all know), and is basiclly getting above himself by daring to dream of being a hero when he has no Quirk. Explicitly, the bullying is focused around his Quirklessness.
I mean, hell, there's at least one mediocre Quirk in the room with that kid with the long fingers; while it's more useful than your freckles example, he's really not going to be a hero off a Quirk like that. Yet, the teacher says that everyone wants to be a hero, and everyone cheers... except Izuku, who is trying not to get noticed. I doubt anyone thinks Long Fingers Kid can ever be a hero, but he can dream that apparently universal dream, the same way most kids dream of being rich and famous, even if the know that they'll probably never be any such thing. Izuku, though? He's not allowed that dream.
Meanwhile, there's Aoyama, who we don't get much information on because Post War, but apparently his life was so miserable that his parents basiclly sold their souls to AFO just to get him a Quirk and thus societal acceptance.
Melissa Shield is an outlier on that dynamic of 'Quirklessness is something that society mocks and beats down on', because she's happy and apparently well adjusted, but there's some things about her which throws that metric off; most fundamentally, she's not from Japan. We don't know what it's like in the U.S., but we know that MHA Japan seems unchanged (bizarrely so, you'd really expect all these upheavals and advanced technology to cause more major changes), beyond Quirks and Heros, from our Japan, and from my understanding (though I'll admit I'm hardly an expert) Japan is generally less accepting of those who fall outside of societal norms, and more tolerant of things like bullying. Whatever it's like to be Quirkless in the U.S. could just be... nicer, than what it's like in Japan, which is canonly shit by all accounts.
And, while we don't see much of her life, the fact that her father's first instinct is to comfort her is telling that it is seen negatively there, at least to some extent. So, with all that in mind, I don't see Melissa as disproving the 'Quirklessness is bad' concept, she's just specifically lucky in not being around a Bakugou, along with being in what is likely to be a more welcoming environment in America and I-Island, along with the fact that we literally don't know her life. For all we know she was bullied for it to some extent, and it just wasn't as bad as Izuku had it.
The fact her work is more accepted than it should be... again, we don't actually know what American/I-Island society is like; maybe she did have to jump through more hoops, and we don't see it. Maybe she 'earned' her place a while ago, and was accept despite her Quirklessness because she's that good. Maybe her scientist father lends her legitimacy/protection from such things. There's a lot of ways to explain that off, but if I'm being honest I don't think that's something Hori actually put thought into, so I'm not surprised her backstory and what shaped her is unknown/more or less non-existent.
On the other hand, Mirio is in a completely different situation than someone born Quirkless, because he had a Quirk. He was a hero, he has a history of success, and had that taken away from him. Of course he's going to be treated differently!
He was normal, is the thing, and so from that lense the natural thing people would think of him isn't contempt for a lesser, but pity. If you look at Quirklessness as a disability, than while Izuku has, what, a birth defect(? Not really sure there's a good example to use, here), Mirio is a veteran with a missing leg.... though, again, after he loses his Quirk he's put on a bus until he gets it back, and even then he's barely there, so... we don't actually know how he was treated.
And all of that brings us to the other way to look at Quirklessness: as a story element. This is the end where so many complaints come from, and it's clear it's an element Hori dropped, and wanted to be forgotten, a long time ago. I've said it before, but MHA is a story with the bones of a completely different story in it; so much of early MHA is built around a lower key, lower power leveled dynamic, in the same vein as the one shot with the older Izuku who never gets a Quirk, one that was rapidly phased out for the newer flashier story... but it was never removed properly, and it suffers from that incomplete separation.
It's the same reason that Izuku gets through the Sports Festival largely with his wits, but not too long after he goes on the field trip and the only way he can deal with Muscular is with raw power, even though (as pointed out by @kingvamps a while ago in a comment) he has, like, a designated weak spot in his eye, literally a, 'hit here to beat him' area, which could have been used as the way a much weaker (Quirkless) Izuku could have beaten his much stronger opponent (if, admittedly, a version that is maybe less overwhelmingly powerful than what we see in canon), perhaps with some help from Kota: because the Sports Festival still has those bones from the original story, planned around that dynamic, where Izuku was presumably Quirkless, and so has to solve his problems with his mind, where by the time we meet Muscular we've completely moved past that into the new story, where, if it was possible, Izuku was never really Quirkless at all, and even if he was it never really mattered to him. Now let's watch him punch good!
(For the record, I'll point out that around that time period is where we transition from Bakugou having some (not enough) consequences to his actions/attitude, to his attitude suddenly being great and awesome, and isn't it funny how that works out?
You can see the bones, again, where Bakugou being a bad person was actually relevant in some earlier draft of MHA, until we reached the point where he was either written out of the story all together, and thus Hori was writing him without that guideline, or his role just became much more important and had to be altered accordingly, and so he, and how people reacted to him, changed out of nowhere to the new standard that has continued from then onwards.
The fact that Izuku's Quirklessness and how it affected him, and his traumatic backstory as a whole, would reflect negatively on Bakugou if it was focused on at all, who at that point seemed to be promoted in the manga's storyline is probably connected on some level to the fact that those factors also stopped being relevant. Though, admittedly, I doubt that that's the only reason why Quirklessness was phased out of the plot, I don't think it's an insignificant reason for it either. While this is technically correct and relevant, it's also something I think is a bit too off topic, so I'll leave it at this for now.)
You're right that, in this final product we've been given, outside of one or two chapters that could have been edited, there's no actual relevance with Izuku originally being Quirkless. It is, for all intents and purposes, a useless story element... but it shouldn't be. There is so much potential to exploring it, so much that could have been done to develop Izuku, Bakugou, and just the setting as a whole, that could have made everything deeper, and more interesting, and one of the biggest problems with the story is this, that a fundamental part of the main character was deemed inconvenient and abandoned.