Alright, I see the sentiment enough in this thread to want to speak to my own perspective on Phantom Blood in particular, and to do it I kind of have to talk about the entire series as a whole and my own history with it.
Stardust Crusaders has always been the pop cultural juggernaut of the series; it's the breakout arc that codified the formula and lead to the strongest merchandising efforts out of any distinct part before or since. That bled into the first ripples of the series to be seen outside of its domestic market: JoJo's Venture not only marks the level of craft Capcom at the height of their pixel art powers wanted and could expend on the license, but its retrospectively slightly off-brand localized title is an artifact of that unknown period when JoJo was just an oddity among others from an English-language perspective instead of the self-perpetuating phenomenon it's seen as now. Similarly, when Viz first put out the manga in the mid-2000s, it was Part 3 they published, in full but self-contained without anything but the series-internal recaps to anchor it to what came before, and no plans that materialized to follow what would come after. The fighting game-derived Dio memes proliferated in nerd subcultures, but there wasn't a sense that the series would ever break out globally--or at least in the English-speaking, largely North America-centric Internet spaces that dictate these perceptions--in the way it had become a celebrated fixture back home.
This is the part where I come into the view of the series, probably around my late teens or so. I don't know what prompted me to start reading it through scanlations (I picked up the aforementioned Viz paperbacks later on)--probably just general omnivorous tendencies as a reader. It puts me in a silly and self-contradictory spot where I could obnoxiously front about being into it "before it was cool" (read: pre-anime) but of course, more than a decade past it becoming a mainstream megahit when understood in its home-grown context. The point is that interacting with JoJo as an English-speaker in those days, as ludicrously famous as it in reality was, was different when it wasn't coming at you from every content creator and influencer direction imaginable; the fandom around it was more isolated and fragmented, experiencing the media through weird and flawed means. The yellowed, machine-lettered Part 3 scans were standard, the unintelligible and since memetic "Duwang" transliterations of Part 4 similarly the only option for interacting with the narrative. I don't miss these things, but the sheer wall they posed for gleaning whatever you could of the work had a filtering (and inadvertently gatekeeping) effect that most people would rather not want to bother with, and who could blame them? I questioned my own interactions with the series through such bizarre and shoddy means, but it also told a story of the passion of the people putting this stuff out there, even if they had not the best technology, the best editorial or graphic design skills, or the best source material to work off of, as well as the people who still wanted to follow the story through such a warped medium. JoJo kept trucking along, and I read all of it that existed at the time--up to whatever part of Steel Ball Run was ongoing then.
Then The Anime happened. Oh, woe! This niche underground comic I like that continually sells millions and drives huge swathes of pop culture is now available for anyone with a torrent program or a streaming subscription to watch! How can I ever feel special and learned and cool about my interests ever again? I'm sure some genuinely felt this (and I can convincingly enough mock the sentiment because I have enough self-awareness to know it's not entirely absent of myself) but the truth is I never much thought about the David Production animation. It raised the profile of the series globally to an unprecedented degree, and now JoJo is the kind of well-trodden, self-defining genre unto itself that it has long been in Japan. Finally there's parity! Just because of how people consume media, it has become the pre-eminent way to experience the series, which I don't begrudge anyone for if their preferences lean in that direction, because as neutrally as I can put it the anime is "perfectly competent" at adapting the source material. I would never take it over the comic, while others may state the opposite. As an ongoing project for the past decade, I've mostly kept my distance to it, and don't habitually re-read the series either. What is JoJo to me then--what would compel the long-term interaction I once had with it and that would prompt musing like this now?
I think it's the first story arc, Phantom Blood, that has most of my lingering affection, that occasionally sets the old passion aflame once more when it crosses my thoughts now and again. It's the series at its best for me in all the ways that matter in the comparative ways it's been told across decades; maybe I wish JoJo as a whole was something different, but in the material that exists as it is this is the closest to a narrative ideal I have seen the series be. A lot of it is due to the specifics of Araki's evolution as an artist and how that shift informs the shape and aesthetic of his stories; this is a point for the manga as far as my interests in the work go since those differences aren't as keenly felt in the more standardized production model of the anime, created over a much shorter stretch of time even if in animation it's also very much a long-runner. Phantom Blood lives and breathes the stereotypes and trends of its time; Fist of the North Star is the common reference point to an influencing peer, but that's a series I want nothing to do with, and I think the crucial point of disambiguation is that JoJo in its primordial state borrows the template of mountainous men squaring off and emoting enormously, which is only to its dramatic benefit as the emotional gigantism is reflected in the language used by the ever-present narrator as well as the visual art that goes along with it--yet it doesn't trespass into the distastefully, violently macho and chauvinistic even as it establishes a definite masculinity as an ongoing narrative force within its own storytelling and presentation. Much of that has to do with what kind of person the lead character is.
Jonathan Joestar is the entire point of JoJo as an ongoing generational narrative to me. He is what makes the appeals to a family legacy and destiny matter in the subsequent stories, the emotional fulcrum from which every other distinct JoJo branches off of and through whom they are measured by, even if they never meet. There is maybe an inclination to view Jonathan as a prototype to a kind of protagonist Araki would go on to write, as he lacks the common characteristics shared by most of his literal progeny: he is not hot-tempered, not prone to mischief, not a social outcast, not eager to punish those who've wronged him with violence. He lacks the kind of easy dynamism that makes jokesters like Joseph easy to both write around, proactively prod along, and for audiences to relate to and root for if not on a personal level then for the sheer interest of seeing them bounce off others. In this purview, Jonathan becomes "the boring one"--heck, he's almost visually identical to Joseph anyway, so there is the feeling that he only matters as a narrative catalyst, for being the First Joestar and nothing more.
As much as JoJo is about the Joestar bloodline, it's equally as much about Dio. Dio the invader, Dio the eternal adversary. Dio is there from the start, and then he dies. He dies several times, yet his influences never leaves the series; echoes of his actions continue to ripple forward and retroactively through the decades that comprise the larger narrative of the series. Phantom Blood, as much as it can be seen as an "origin story" to decades of twisty continuity, is also the only place in which Dio Brando the person appears in. It has nothing to do with his transformation into a vampire partway through it, or the sole means of his continued existence in later arcs. The series itself knows this, as those later incarnations are signaled by the bold typeface of the DIO mononym--he is a coordinated performance of hackneyed ideas and concepts of villainy; an engine of choreographed theater responding to an audience that's always there in his mind. Part 1 Dio is not invulnerable, and he is not so polished in the ways that the character places importance on, in appearing sufficiently sophisticated to satisfy his own ego. He struggles to execute upon his scheming, he panics when resisted, he retreats into drink in the ways he hated his father for, and curses his own weaknesses. The DIO that consumes the future of the Joestars is not seen through this lens as he builds up an industry of evil around himself to protect his own image from ever again seeming fallibly human, and it's how he shields those same weaknesses that never truly left him. The one person who ever made him confront those aspects of himself, who truly defeated him in a way he could not accept, was Jonathan--unassuming, quiet Jonathan, the object of Dio's years-long gaslighting and psychological torment in their youth, and the one person he could not break. It follows him to the end of his days, as it doesn't really matter that it's Jotaro and Joseph he faces--they're only extensions of Jonathan to him.
Jonathan is a flat character in his way, but he is not unchanging; Dio's arrival launches the arc that sees him transform himself from an astoundingly privileged and pampered gentry heir into becoming someone who's cognizant of his own privilege and comes to see it as a duty to live up to instead of a silver spoon to cling from. The mistreatment of Jonathan by Dio in their shared youth helps him ascertain his own ideals, while Dio descends further into his own insecurities and paranoia. Yet they are raised as family, as brothers, and that intimacy never leaves the relationship no matter what kind of violence occurs between them. Jonathan can't forgive Dio for the trauma he's inflicted on him, and he also can't disassociate the love he still bears for the man who was his brother; the pain of futilely reaching out to your family is palpable in their deteriorating sham of a family dynamic. This relationship is everything that Phantom Blood is, and the sense of interpersonal intimacy is almost entirely absent from every JoJo story thereafter. In a way, it reflects the published history of the series, as in its nascent form there were no expectations, no clear plan for what JoJo could even be. It's an experimental character piece told in the form of a martial arts horror comic, with none of the rigid formalism that define the later story arcs; it's unburdened by formula as the series could never be again after the introduction of Stands. I don't care about Stands as a vehicle for fights, because I don't care about the fights except as a vehicle for character interactions, and that is a balance that cannot be met as the nature of the comic becomes a weekly suspense puzzle of figuring out what's killing me now and how can I outsmart it before it's too late, before whisking off to the next multi-chapter fight. The JoJo arcs that work better in this framework are the ones that profess that same character and setting-based stability and intimacy that informed the series at its outset--Parts 4 and 6, namely--and it's a quality that marks the individual highlights within those stories. People latch onto Let's Go Out for Italian from Part 4 and deservedly so because it puts the focus on what's inherently the most interesting about the setting it's told in: the people in it, in all their weird mundane fixations.
Why does Jonathan's portrayal land so emotionally hard, then? He is an archetype through and through, and there is an argument to be made that he's too "flawless" to come across as exceptional. It comes down to symbols and aspirations for me: Jonathan sets the example that no JoJo since has ever met, and it's not for want of trying; the series wallows in sentimental iconography about him to communicate that he matters as someone to live up to. All the JoJos after him, if they compel as characters, do so because their imperfections shape who they are: Joseph the rascal; Jotaro the terse stoic; Josuke the goof-off; Giorno the... look, I can only do so much; Jolyne the angry resenter. All of them are heroic for reasons of narrative and who they oppose, but they have personal failings everywhere in their lives: Joseph's infidelity and Jotaro's misogynist outbursts are extensions of their characterization of the kind of person that is "fun to read about" as a protagonist of a serial like this, and also the kind of boys' comics personage that's permissible and even expected to feature as the lead. Jonathan is exceptional because his overwhelmingly defining trait is his empathy, respect and love for his friends, family, and yes, his enemies. Women don't get their stories told in JoJo (even if Stone Ocean has its merits) and Erina is completely ancillary to the actual emotional focus of the story, but at the end, when the literal disembodied head of his brother is burrowing its tendrils into his flesh, Jonathan's priorities are equally reserved for the mockery of brotherhood before him and the love of his life; the feelings he has for them are the same. Jonathan could have been a bully, he could've been a "justified" avenger, but even in aspects where the series traditionally fails, his presence makes those same plot beats feel a little more acceptable and inclusive just through the nature of his character and what he represents. There are so many JoJo stories that end with the despotic villain getting their comeuppance in the most over-the-top, hypnotically gruesome and in many cases, never-ending means of violent punishment they are now imprisoned in as symbolic purgatory for their crimes: Phantom Blood is the only one where a man ends his life smiling and embracing his own killer out of love.
I don't really know where my own relationship with JoJo stands these days; it has become more retrospective by default than anything. Part of it is because I have little interest in the adaptations that continue, as well as in the comic itself because of that same evolution of Araki as an artist and author that characterizes and delineates the different arcs even more strongly than the literal boundaries do. I don't need to be interested in his later work, and he is not obligated to cater to the preferences of his audience; he has enjoyed a long career and done many incredible things during it, so it's up to everyone to pick and choose what they may from the catalogue. There are fans for each and every Part who value a different one the most, and everyone's personal story with the series informs that call. At this point, I've comfortably landed on mine.