Jotaro's actions in this part. Was he holding back on telling Jolyne about DIO since he didn't want her to get into any danger, or was he going to tell her anyway knowing that the time would come one day? There's also the case of whether or not he knew that some of DIO's henchmen were still lingering and that DIO had a backup plan. If so, than this would also explain why he was so intent on recovering the two Stand arrows in Morioh and sent Koichi to Italy to interrogate Giorno.
Pucci's relationship with DIO is often questioned by many readers. The canon suggests DIO Homoerotic Subtext with Pucci was him tempting him, just to see if he could be the "friend" he was looking for, not tempted by carnal desires, meaning that by all intents Pucci should be asexual... however, even by Ho Yay standards, many fans heavily doubt this, and question what exactly was DIO looking on him.
Related to the above, was DIO's friendship with Pucci genuine, or was it more of his manipulative nature and merely saw Pucci as a means to an end? Another interpretation was that DIO intended on manipulating Pucci from the start, but ended up genuinely befriending Pucci.
Anti-Climax Boss: Pucci ends up being this. After effortlessly killing the main cast bar Emporio, what finishes him off? Emporio, the least combat efficient of the group, surprising him with Weather Report.
The maximum security ward portion of the part is often cited as the biggest drag in the entire part. While it starts decently enough with the Planet Waves battle it quickly nosedives with two of the most reviled battles in the entire series in Dragon's Dream and Yo-Yo Ma. It does pick up once Pucci finally enters the scene but by then it's almost time for this portion of the story to end.
A lot of the arcs towards the end are really long, ranging from about 10 to 12 chapters in length. Most notable are the Bohemian Rhapsody and Heavy Weather arcs, which are some of the longest non-final battle arcs in the series. It doesn't help that for many the Stand battles in this part don't have much going on in terms of actual fighting.
Author's Saving Throw: According to some interviews, a lot of the reason for the largely female cast of Stone Ocean is that Araki was disappointed with how so many other of his other female characters ended up being either Neutral Females or Faux Action Girls, and he wanted to try to break away from that.
Badass Decay: Jotaro suffers this hard. First, he spends the majority of the part in a coma, and when he finally returns, Pucci unceremoniously kills him.
Anasui. Is he a funny and interesting character, or is he an unlikable jerk whose obsession with Jolyne comes off as him being too creepy?
Pucci is divisive amongst the fanbase. One camp likes him for being a genuinely sympathetic villain, who surprisingly gives a degree of humanity to DIO of all people, not to mention the various stands he possesses. On the other hand, other fans dislike him for Jumping Off the Slippery Slope and lose sympathy for him once he unlocks Made in Heaven and kills off most of the main cast. Not to mention the fact that his actions led to Stone Ocean's controversial ending.
The Sons of Dio are an interesting example. All three of the characters are relatively well liked by the fanbase, each being considered very well-written. Rather, what fans are divided on is their status as children of Dio. Some find this an cool idea that was well executed, while others feel that having them be directly related to Dio was a bad idea since it robbed Giorno of the unique quality that made him stand out; the fact he had the traits of Jonathan and Dio. Then their's the 3rd group that like the concept behind them, but feel that it could have been executed better.
The ending, big time. Was the universe reset an emotional sendoff to parts 1 through 6 that acted as a satisfying conclusion to the long saga or was it a cop-out ending that made the wholesale slaughter of the protagonists pointless and felt like a contrived means of concluding the initial continuity?
Stone Ocean has quite possibly the strangest, most out-there stand powers in the entire franchise. While some applaud them for being among the most creative abilities yet, there's a lot of contention as to whether Araki took it too far, with many feeling that some of them are SO kooky that they don't make sense, with Heavy Weather being the most cited example. It's to the point where Stone Ocean is often accused of having the weakest stand fights in the series.
"Common Knowledge": No, Made in Heaven doesn't kill everyone in the universe. If you're alive when Made In Heaven resets the universe, you keep the memories you had before. It's only if you were already dead when the reset happens that your soul is reshaped into a different version of yourself.
Contested Sequel: Stone Ocean as a whole is arguably the most divisive and contested part in the series. Some fans love it for its general craziness, main cast, sympathetic main villain, and an emotional ending. Other fans consider it one of the weakest parts, citing a bizarre plot, mostly forgettable minor antagonists with some like Dragon's Dream and Yo-Yo-Ma being outright disliked, with fights that are a step down from the ones in Vento Aureo.
Darkness-Induced Audience Apathy: Given that practically every single one of the main characters except for one ends up getting killed off and Stone Ocean ending with a universal reboot, this is likely to happen in the eyes of some readers.
Anasui gets this from fans who prefer to ship Jolyne with other characters. It's not hard to find fanworks of him being a Butt-Monkey or even just plainly ignored. To be fair, he did kill his previous girlfriend, and one Jolyne doesn't show much canonical attraction to.
Jolyne's mom is not treated nicely by some diehard Jota/Kak shippers, although some are more sympathetic, partially because the idea of Jotaro pining after a dead teenager would get uncomfortable, and partially because he treats her (as far as we can tell) in a standoffish, dismissive manner, which makes her cry in almost every scene. It turns her into a bit of a woobie.
Draco in Leather Pants: Pucci gets this treatment as much as Dio. It does help that he is more sympathetic than other antagonists and there are some fans who found his motivations more understandable than the protagonists. But then again we are talking about the guy who killed all but one of the main cast.
Emporio has slowly started becoming a popular character. Unlike other protagonists in the series his Stand is rather weak and he doesn't do much in the way of action but many fans ended up feeling really bad for the poor kid especially after the ending. Being the one who inherits Weather's Stand, defeats Pucci and finally ends the Joestar's never-ending battle certainly made him a favorite among readers.
Rykiel is quite beloved among the fanbase for inheriting his fathers determination and being the most sympathetic of Dios sons (with the exception of Giorno).
Estrogen Brigade: Being the only part with a female protagonist and featuring a mostly female cast, this part is naturally very popular among the female portion of the fandom.
The general assumption is that Jotaro met his previously-unmentioned wife in college, and that she's a marine biologist like himself (albeit one who probably gave up her career to devote herself to raising Jolyne).
Many fans like to generally assume that Jotaro's alternate counterpart's name is "Qtaro", a reference to the Sue Donym that he gave to Enyaba in Stardust Crusaders.
At one point, Jolyne reads a comic◊ with an art style that resembles Thoth, leading fans to theorize that Boingo grew up to become a successful illustrator.
Fan-Preferred Couple: At least in the West, Jolyne/Ermes is far more popular than Jolyne/Anasui, which is canonical in the reset universe, in part because it parallels the other popular Bash Brother ships from previous parts, like Josuke/Okuyasu and Jotaro/Kakyoin. Foo Fighters is often included in as a One True Threesome.
Fashion-Victim Villain: Character designs were pushing it in Part 5, but by this point, there was essentially no limit to what could be considered clothing in Jojo. Special mention goes to Miu Miu's heavy wrinkled sweater resembling a set of small intestines with a pair of eyes, Rikiel's cow-patterned jumpsuit with a chin hood and head suction cups, and D an G's multi-colored toga that might as well be a rug.
Whitesnake has "GΔCT" written all over its body to represent the four nucleobases that bond DNA. Astute geneticist readers will notice that the delta sign (Δ), where A should be, is the sign of gene deletion aka a missing genome, foreshadowing that Whitesnake/C-Moon aren't the "complete" forms of Pucci's stand.
When Pucci's C-Moon is active, he was briefly able to move in Jotaro's stopped time to dodge the spear Jotaro threw at him. This is because gravity can affect time, an effect known as gravitational time dilation.
Germans Love David Hasselhoff: Stone Ocean is perhaps the least popular part in Japan, given how it strayed away from the shounen tropes of previous parts, while still demonstrating some of the issues inherent with a weekly shounen format. In the United States, however, it has a much larger fanbase, with many seeing it as a worthy precursor to Steel Ball Run. A lot of elements in Stone Ocean are also more appealing to Americans such as the fact that it takes place in Florida, and is a prison battle story much like another manga that is more popular in the United States. Jolyne herself is also one of the most popular characters in the United States with about as large a following as Joseph and Josuke. It helps that she's a very atypical female protagonist: She's openly flawed, crude, and has a chronic masturbation problem, which makes her stand apart from many other female protagonists, who are often portrayed as "too innocent" for sex, or who writers are afraid to give flaws.
The carrier bird being named "Savage Garden" simply passed everyone's radar... until "I Want You" was used as the ending theme for the Part 4 anime and now many have come to believe that Araki predicted the future. Made even more apparent by the fact that the band Savage Garden is mostly affiliated with JJBA these days because of it.
Foo Fighters was a mass of plankton pretending to be a human. 7 years later, Foo Fighters releases a song named "The Pretender."
Ho Yay: Dio/Pucci. While most of Dio's male henchmen were practically infatuated with the guy (including one who appears in this part), Pucci was the most fanatically loyal of his henchmen. There's also a flashback where Dio is in bed with Pucci.
Inferred Holocaust: While the universal reboot doesn't directly kill anyone, as detailed under "Common Knowledge", the time-accelerating effects of Made in Heaven would have severe repercussions beyond what was already shown.
Implied with Foo Fighters, who admits in her final moments that all she ever wanted was to be accepted as a normal person after inhabiting a human body.
Weather Report much like Pucci was never told that he had a twin brother and as such never found out that the girl he liked was actually his sister. It only gets worse when he had to see the girl he liked die in front of him while at the same time losing his sister without knowing it. And after all that he became ostracized from society because of the abnormality of his Stand power. And to top it all off, just as there's a sense of hope for him to reform with his allies, he is killed by his brother.
Until Funny Valentine was introduced, Pucci was the most sympathetic villain in the entire franchise. It all comes full circle in his backstory where it turns out that the only reason he turned to villainy is that at birth he was convinced his twin brother died and no one ever told Weather the girl he liked was their sister.
While Rikiel is Affably Evil and Ungalo is utterly unsympathetic, Donatello Versus fits well into this trope. He's an utter narcissist who is willing to kill children for the crime of getting in his way, but he was also arrested at 13 for a crime he didn't commit, and went to a prison where the guard frequently beat him, nearly causing him to die. Considering all the shit he went through, it's not too surprising that he turned out so rotten.
Jolyne/Ermes in some of the post-chapter sketches, and even in one of the manga volumes, who are shown in physically intimate poses together.
Guess uses her Stand to turn Jolyne into one of her dolls, forces her to speak in a "cute" manner, and after her defeat swears eternal loyalty towards Jolyne.
Magnificent Bastard: Enrico Pucci is a charming priest who was plunged into despair after racists murdered his sister due to his own mistakes, and the extremely unfortunate set of circumstances that brought about her demise drove Pucci to hate the idea of an unforeseen future and "fate." Coming to idolize DIO, Pucci collects the man's thoughts and plans for a new way of life called "Heaven," and, after handily pulling the strings of everyone in Green Dolphin Street Prison—taking time to try to genuinely help the prisoners there even as they attempt to rob him blind—Pucci uses his upgraded Stand "Made in Heaven" to begin his final plan: To force every human being to live out their whole lives, and see the entirety of the universe's lifespan, then relive their lives knowing their and everyone else's fates, this enabling them to never be surprised or broken by life's events, knowing beforehand all that will happen. Pucci is easily the most well-intentioned and genuinely caring Big Bad in the franchise, wanting to simply end the pain that comes with not knowing one's fate, and even while dying a torturous death tries to ensure his "Heaven" will carry on, even at the cost of his own life.
Memetic Molester: As if DIO wasn't already a Fountain of Memes, the flashbacks involving him with Pucci in this part have caused him to enter this status as well, especially since Pucci was only 15 at the time of that flashback.
"Do You Believe in Gravity?" note Pucci's signature line in this part that is one of the most quoted lines in the series a la "Speedwagon withdraws coolly"
"Pucci the Gay Black Priest" note A title given to Pucci due to the subtext of his relationship with DIO. The lack of characters that can be considered "black" in Jo Jo also grants him extra attention.
What's wrong, Pucci? Why do you want to reset the world?note An exploitable comic: the first panel shows Jolyne asking Pucci that question, followed by a panel of the priest superimposed over an image of something the meme's creator dislikes or disagrees with as the answer.
"Where the fuck is Mickey?!" and "For fucks sake, if there's no Mickey this shit ain't Disney!"note Anasui's comments in the beggining of the infamous Bohemian Rhapsody arc
Some fans joke that Jotaro's true wife is a dolphin (given his job as a marine biologist to protect sea life), rather than a human female.
Jotaro being an Disappeared Dad throughout Jolyne's life. While Jotaro's parenting skills nothing to brag about, fans take things up a notch by portraying him as being deliberately neglectful towards Jolyne even though it's made clear that all in all Jotaro deeply loves his daughter.
The famous scene of Pucci and DIO in bed together. The subtext is more ambiguous at most and while Pucci is indeed undyingly loyal to DIO, its implied that he loves DIO in a more platonic way. Yet fans like to portray Pucci's sexuality as his defining if not only character trait.
Rooting for the Empire: Unlike previous villains in the franchise, Pucci has well-intentioned motivations for his goal and a sympathetic backstory. There are some readers who actually wanted to see his victory over the protagonists... It does help that he came close to killing off all of the protagonists minus Emporio, and was successful in creating a new universe... just not the one he wanted.
The Scrappy: D and G's Stand "Yo-Yo Ma" who is often put up there with Arabia Fats as having one of the least interesting fights in the series. A lot of the dislike comes from the fact that the pacifist nature of "Yo-Yo Ma" prevents the fight from going anywhere and the arc ends up getting repetitive.
Likewise, the Stand User fought before him, Kenzo, and his Stand, Dragon's Dream, are also extremely hated by the fans for being a boring fight that ends up feeling like a complete waste of time.
Song Association: All major characters naturally are associated with their musical reference, but Weather is frequently represented with Jamiroquai songs, due to resembling the band's mascot.
Squick: Jolyne using Stone Free to unravel her own body is really unsettling to look at, especially for readers who have trypophobia.
They Wasted a Perfectly Good Character: Foo Fighters especially given her sheer popularity. In and despite of being one of the main characters she only gets one major fight which is really just helping Jolyne defeat Kenzou. Not helping is the fact that quickly afterwards she is killed by Pucci only halfway through the story and has no counterpart in the new universe. She even doesn't even get to be playable in All Star Battle and Eyes of Heaven.
Enrico Pucci's actions attracted to Florida three young men who were all DIO's sons, but Giorno was nowhere to be seen despite DIO's blood in him. Araki hints that Giorno may be in Florida after all, though the reason he wasn't drawn to the priest is unknown. It would be a good occasion to make the character interact with Jolyne.
While it's understandable that Joseph is simply too old for action anymore, there are some fans who question why Josuke and Giorno were not present in the finale. Pucci had created a global catastrophe so you'd expect the Speedwagon Foundation would give Jotaro as much help as they can. It doesn't help that the Speedwagon Foundation knows of both of their existences and in Giorno's case Araki has hinted that he was in Florida at the time. Bringing in Giorno and Josuke could have also created a crossover situation à la The Avengers. Having Josuke and Giorno in the finale could have also allowed Okuyasu, Koichi, Rohan, Yukako, Mista, and Trish show up and allow all of these characters to interact with the new characters for this part. In fact, in the case of the Part 4 characters, readers would finally be able to see what they've been up to since the ending, as they were almost completely ignored in Part 5, and so canonically are in their mid to late twenties and likely adults with careers and maybe even families of their own.
Too Cool to Live: Practically the entirety of the main cast barring Emporio is killed off by Pucci, though two particularly stand out. The first being Weather Report, the guy who came the closest to killing Pucci, and resident Showy Invincible Hero Jotaro himself.
What Do You Mean, It's for Kids?: Often described as the part where Araki was preparing himself to leave Shonen Jump. While Vento Aureo had its moments, Stone Ocean is filled with even more gratuitous violence, many Stands with abilities that are outright frightening, tons of sexual content, and having a cast of mostly older females.
Jolyne, starts out really hostile towards Jotaro since he was absent for most of her life, even during times where she needs him the most. The whole part revolves around her trying to restore Jotaro's memories and Stand, only to die at the end just as she could finally bond with her father. In the new universe, however, she is living a normal life and is very likely having a better relationship with her father.
Emporio, who was born in prison, and lost his mother at a young age. He spent his entire childhood in Green Dolphin Prison because he had nowhere to go. It only gets worse in the end when all of his friends and Jolyne the closest he's ever had to a "mother" die and he is the only resident of the new universe to remember anything about the old one.
Jolyne's mom, who had a strained, most likely mostly long-distance relationship with her husband, and whose daughter kept ending up in prison, making her worry constantly. She sort of ends up by the wayside by the end, never getting a proper reunion with either Jotaro or Jolyne (although her reboot counterpart is implied to still be married to alt-Jotaro by the end, and her daughter "Irene" is in a happier situation than Jolyne was).