Even though people were happy to see that Peter wasn't completely dead, Ghost-Peter's presence had a tendency to irritate the fandom due to being ineffectual. However, when he was "killed", people were more than ready to grieve for the character. This being said, his post-resurrection self is widely considered to be better as a character.
The series end with Carlie, literally, getting Put On The Bus. She leaves New York, still not completely cured of the Goblin Formula. Messages from Slott around the time of the story seemed to indicate there's also no plans to bring her back.
Arc Fatigue: Let's just say that there are plenty of people who think the story overstayed its welcome. The big complaint is that it took nineteen issues for someone to figure out that Otto is impersonating Peter, especially in a world where mind control, possession and/or body surfing is so common that the police should have a code for it.
Audience-Alienating Premise: Taking one of the nicest, most upbeat characters in the Marvel Universe, having him murdered while his loved ones express their hate for him, and replacing him with a prominent member of his Rogues Gallery hasn't exactly sat well with some fans.
The implication that Otto was planning to seduce and have sex with Mary Jane whilst in Peter's body did not go down well with readers at all, as such a situation would be considered akin to rape. This also wasn't too much longer after another supervillain impersonating Peter apparently had sex (or at least had an intense make-out) with a female love interest (Chameleon and Michelle Gonzales), which a number of people pointed out, could technically be classed as rape due to the consent involved. Thankfully, the following issues, Otto ends up developing some morality and breaks things off with MJ before anything more happens.
Issue 31 has the returned Peter doing quick damage control over all the bridges Otto previously burned. He's back to being on good terms with his Aunt May and Jay, Spider-Man 2099 immediately believed him, The Avengers seemed to have listened, and MJ and Carlie both understand but have washed their hands of him nonetheless. Of course, there were segments of people feeling it all got solved too quickly, and others were not happy that nothing between Peter and Black Cat was cleared up.
Awesome Ego: Fans of the series tend to consider Otto to be this.
When the title was announced, Superior Spider-Man had some people willing to give it a chance, and some not going for it based on the concept itself. Some hate it with a passion and others think it's an interesting development. A lot of people were particularly sore with the way that Peter was killed off in the first place, along with the idea that Doc Ock, a villain who had nearly turned the planet into a Death World, would be taking over.
The Reveal from the end of Issue 1 - that Peter Parker is along for the ride but unable to do anything other than stop Doctor Octopus crossing certain moral lines - received praise for how unexpected it was, but also received plenty of hate for being a fairly obvious twist people could see coming, and coming in the first issue.
Subsequently, how often Ghost-Peter actually appeared, some like it while others just want him to shut up.
Then there's the matter of Otto removing Peter from his mind, which basically made people on both sides more vocal about their stance on the series.
Fans of the comic are divided on whether the story was better as a Redemption Quest or if it is better as a story with a Villain Protagonist, as the former is pretty much dropped for the latter.
Fans are conflicted over the way that the final confrontation between Peter and Otto was handled, with one group seeing it as a genuinely moving Redemption Equals Death moment and the logical progression for the storyline, another group seeing it as an Anti-Climax that goes against what the story was building up to since the end of the "Superior Venom" arc, and another group is just relieved that Peter's back and the arc is nearly over.
Was much of the dark content in the series meant to get people into the story by means of shock value, or to develop Otto as a character? It depends on what part of the Spider-Man fandom you ask.
In the story, the public's positive reaction to Spider-Man straight up killing someone reeks of this - especially considering that a pair of "What-If?" stories published in 2010 and 2011 showed that things would end very, verybadly if Peter chose to kill a supervillain.
Catharsis Factor: While this is somewhat cancelled by the ensuing murder, SpOck successfully outsmarting Massacre by freeing the hostages he relied on as his back-up, then promptly Curb-Stomping him is greatly satisfying, giving the killing spree we saw the man commit.
Critical Dissonance: Despite how polarizing the run was, Superior was consistently topping the Marvel sales charts all throughout its run.
Critical Research Failure: Jonah Jameson somehow manages to order a death penalty for Spider-Slayer. This makes no sense, since the prison holding him belongs to S.H.I.E.L.D and even if it didn't, a mere mayor does not have such authority and New York got rid of its death penalty.
Darkness-Induced Audience Apathy: As far as the source material goes, a number of fans stopped reading due to the direction that the character took. This stance was cemented with some by the first annual, or even earlier with Issue 9. Several of these people also claim that the series relied too much on shock value to boost sales instead of telling a satisfying story.
Designated Hero: Otto isn't meant to be a straight-edge hero, yes, but a number of his actions aren't heroic by any measure, such as killing a defenseless criminal on live television or (briefly) wiping the last remnant of Peter from his mind.
Designated Villain: Peter (at least in Otto's eyes) is initially portrayed as being in the wrong for wanting control of his body back. It doesn't help that his only vice (not wanting to help save the life of a little girl out of fear that it'd reveal his presence) never would have happened if Doctor Octopus hadn't tried to cause the apocalypse in the first place.
Dork Age: While people warmed up to the series after it started (probably in no small part, due to the existence of Ghost-Peter), others were still not satisfied, claiming that Ock is out-of-character, Ghost-Peter is annoying, the supporting cast suddenly became idiots, and the quality of the writing didn't improved much from when Dan Slott was writing regular Peter.
Draco in Leather Pants: To this day, despite how contentious the arc was, there are fans who legitimately argue that Otto was a better Spider-Man than Peter. His more immoral actions gets written off as the Ends justifying the means.
Disney's purchasing of Star Wars, after Ghost-Peter first appeared & resembled the Force Ghosts seen in that series thanks to simply coloring Ghost-Peter a pale blue. Cue jokes about how Peter Parker was strong in the Force, and that Superior Spider-Man was the first crossover between the now-owned-by-Disney Marvel & Star Wars universes.
After Kaine killed Otto in the Clone Saga, Peter donned his gear for a short-lived stint as "The Amazing Octo-Spidey◊".
Near the end of Kraven's Last Hunt:
Kraven: I "killed" you, Spider-Man. Buried you. And after I "killed" you, I took your place. Spider-Man: You drugged me, Kraven. Threw me into a state simulating death. Kraven: You could just as well have been dead had I wished it. I only allowed you to live, so that you could know that I "killed" you. That in donning your costume, in replacing you, I proved myself in all ways your superior.
Carlie almost getting a Goblin tattoo becomes this once Otto's spider-bots are hacked to ignore anybody with one.
Otto successfully performs brain surgery on a young girl who was affected by his global warming scheme and receiving her stuffed doll as a thank you. When Otto tells her he can't accept such a thing, the doctors tell him that she has already replaced it with a Spider-Man doll.
When stranded in the year 2099, Otto has a holographic avatar of Anna Maria guiding him as a reminder of what he left back home.
Otto: "Call me 'Otto'. I have never heard her speak that name. It would be... motivating."
Informed Wrongness: A number of Peter's arguments in issue 9 are dismissed by Otto rather quickly, even though a number of them have merit.
Back when it was announced, it got so bad that there were even death threats over the replacement of Spider-Man.
After Dan Slott "accidentally" tweeted Ryan Stegman a message hinting that the Superior Spider-Man was Miguel O'Hara/Spider-Man 2099, he received so much hate after this was confirmed as a Red Herring that Slott had to actually apologize over the matter and reassure readers that Miguel would eventually make an appearance in the series.
The Ship Tease for a reunion between Mary Jane & "Peter", with readers pointing out that any relationship would effectively mean, unless Otto reveals he's the one in Peter's body, the moment anything happens would effectively mean Doc Ock was raping Mary Jane. It's all resumed very quickly when Ock gets a guilt-trip and breaks things off with MJ before they go that far.
Now, there's Issue 9 with the erasure of Ghost-Peter.
Jerkass Woobie: In spite of being seen as largely unsympathetic, people felt bad for Octavius in the "Goblin Nation" arc.
Like You Would Really Do It: A Double Subversion occurs with Peter Parker, who's shown as a "ghost" through the first nine issues - then, he is erased from Otto's consciousness, only to return when Otto tries remembering Peter's past. On a meta-level, this is played straight - plenty of people knew that he'd come Back from the Dead in time to make money off of The Amazing Spider-Man 2.
Otto can come across as this at times, such as his defeat of the Spider-Slayer.
Roderick Kingsley is still this. The Hobgoblin that the Green Goblin killed with his own hands in issue 19 turned out to be Roderick's butler, Claude, who he brainwashed to pose as him. The issue concludes with Roderick resolving to lay low while building up his criminal empire, all the while brainwashing yet another hapless individual to serve as his fall guy if a future situation calls for it.
The Goblin King, who not only anticipated many of Otto's actions and had several countermeasures prepared against them, but is shown effortlessly toppling his little empire, leaving his adversary in a state of shock. There's a reason people were Rooting for the Empire.
Moral Event Horizon: There are a number of potential crossings for the title character. When (or if) this trope occurs in the story depends on the reader.
For starters, there are fans who will point to how Otto stole Peter Parker's life in the first place and his plan in Ends of the Earth as evidence he'd crossed it long ago and no-one should be surprised at his actions as Spider-Man. Ends of the Earth is a particular sore point, as it was Otto's last appearance before the Dying Wish arc, and featured him trying to kill most of the life on Earth. In addition, the entire Kill and Replace gambit that he had carried out immediately before becoming a superhero doesn't really leave him in a sympathetic light.
Issue 9 is a big example, because he ends up (temporarily) erasing Peter's existence entirely instead of simply trying to subdue it, and gloating about how he's finally free.
In Superior Spider-Man Annual, he decides to torture Blackout to study him in a Mengele-like fashion after Blackout had previously kidnapped and was planning to torture and murder Aunt May. To elaborate, he rips out his teeth and fingernails - which aren't presented as a heroic actions in the slightest.
Stealing the Venom symbiote from Flash Thompson simply because he thought he could make better use of it.
Massacre murdering Doctor Kafka.
My Real Daddy: It's somewhat common to find fans who do not enjoy Slott's SpOck in Superior, but rather enjoy Yost's in Avenging/Superior Team-Up.
Narm: Doc Ock and the Green Goblin's friendship montage, which is broken up by an ideological argument that ends with Norman infecting Otto's ex-fiance with AIDS.
Nausea Fuel: The torture scene in the Annual. To elaborate, it involves Otto hanging Blackout up on hooks and tearing out his teeth and fingernails.
Older Than They Think: A Spider-Man villain thinking he has killed the hero and then donning his costume to prove he's a superior Spider-Man than the hero was done in Kraven's Last Hunt, albeit in a far smaller run of issues and to much less controversy and divisive response.
Replacement Scrappy: The "Superior" version of Spider-Man became this before the first issue was released. Word of God claims that this is deliberate. Dan Slott wants to take Spider-Man's Hero with Bad Publicity element to a meta level. It says quite a bit about the character's status as this when more people were celebrating his death than mourning it.
A substantial amount of people actually want Otto to stay Spider-Man, or at least a part of the Spider Family.
On the other end of the spectrum, a large section of the fanbase is now rooting for anyone who's against SpOck. Anyone. Yes, that includes the GoblinKing. Solicits for the "Run, Goblin, Run!" arc make it seem like this is the point, and by the time SpOck started using the Venom suit, some people pretty much stopped supporting the character in favor of his enemies.
Carlie Cooper was back to being this again, thanks to being the only supporting cast member to deduce Otto's impersonation, ahead of characters who had known Peter for much, much longer. She also earned herself some bonus fan hatred for blaming Peter for the time she turned into a giant spider-monster, claiming it wouldn't have happened if she hadn't known him. Since nearly every person in Manhattan became a spider-monster whether they knew Peter Parker or not, the logic was deemed rather flawed. Although, to be fair, Carlie was only able to deduce this was because Peter flat-out told her ahead of time when he was in Otto's original body, and even then it took her a while to actually confirm this.
There are those who feel that Otto became Dan Slott's Superboy Prime. After Issue 25, where Otto with the Venom Symbiote is being shown to effortlessly manhandle the Avengers (including Thor), this is cemented even further.
Otto masturbated in Peter's body. Ghost-Peter is understandably grossed out by this.
Doc-Ock was once in love with Aunt May, and it's canon he still has feelings for her. He's now posing as her nephew, the one she raised as if he was her son.
Take That, Scrappy!: There are a number of "What the Hell, Hero?" speeches towards Octavius throughout the story - a number of which are cited by the Hatedom as reasons that Octavius isn't a good replacement. Otto had enough people hating him that plenty were overjoyed when the Goblin King started to make his life a living hell.
The Spider-Island arc seemed to be the first step in reuniting Mary Jane and Peter Parker, but this was thrown out the window once Otto took over. This is a Justified example, given that there would be plenty of Unfortunate Implications about Mary Jane and Otto-posing-as-Peter getting together - especially in terms of a sexual relationship.
The Redemption Quest aspect of the story is thrown out the window about nine issues in, which, depending on who you ask, undermines the whole point of the series. There are those that think the storyline would have worked better if it had been shorter and if it had kept focused on this theme.
Some even say that the series would have been better if another character had been placed in Peter's shoes. J. Jonah Jameson is commonly cited as one such character.
There are those that feel as though Otto's decision to Face Death with Dignity and relinquish control back to Peter denied the audience the satisfaction of seeing a rematch between the two.
Some feel that the ending was wrapped up much too quickly, and that Peter didn't really have to deal with the repercussions of Otto's actions.
Octavius tends to fall into this. Given that he had stated that he wanted to kill over 6 billion people and that he hijacked his archnemesis's body while leaving him to die painfully, it's hard to give the character any sympathy, even when he states that he wants to do good.
As the comic goes on Otto seems to be moving into being intentionally unsympathetic as he commits more and more evil acts in the name of "justice", especially after he screwed over the completely innocent and good-hearted Flash Thompson to get the Venom symbiote. Of course, whether that was intentional to begin with or if it was made in response to fan complaints is up for debate.
Remember how Mary Jane and Otto-Peter went separate ways so that Otto wouldn't be considered a rapist for impersonating Peter Parker? This was thrown out of the window in Issue 22 when he had sex with Anna Maria Marconi - which would officially make him a rapist, also according to Ernst. Dan Slott disagrees, pointing out the following:
"Anna Maria Marconi only knows Peter Parker as this Otto Octavius person, and right off the bat, when they have their first meeting, she's like 'wow, I thought you were just this slick veneer, this handsome Peter Parker type guy, but you're an Otto Octavius genius, and I like that.' She has looked right through the veneer to this guy on the first real sit-down the've had. So if there's chemistry, she has it with... well, with Otto Parker. That's who she has chemistry with."
Similarly, Tom Brevoort responded to a question of whether or not Otto raped Anna-Maria with "She never knew him as anything other than Peter Parker, and she didn’t know Peter Parker. So no."
What An Idiot: A common complaint about many supporting characters was that nobody seems to recognize that anything's up with Peter until it becomes blindingly obvious. This is probably most evident with Mary Jane, who had been able to easily spot Peter/Spider-Man impostors in the past. In MJ's defense, the other impersonators (Chameleon and Kraven) didn't have access to Peter's memories like Otto did - though this argument doesn't hold up as well once Laser-Guided Amnesia kicks in on Otto's part. Although at this point MJ had distanced herself from Peter for the most part.
Win Back the Crowd: Predictably, Peter's return incited this with many fans, especially with Otto admitting that Peter was a better Superhero than he would ever be.
As mentioned above, while the first issue of the comic was generally well-received, it was also criticized by some for immediately setting up Ghost-Peter, the plot thread that would eventually get to undoing Peter's Comic Book Death.