Anticlimax Boss: Kraven the Hunter. He's built up as a highly skilled warrior who decided to take down Spider-Man. Peter isn't even remotely interested in fighting him (he'd just beaten Doctor Octopus at the time) but when Kraven insists, Peter simply dodges a few times then knocks him out with a single blow. Instantly lampshaded by Spider-Man.
Peter: Huh. I thought he had super powers or something. Showbiz phony.
Arc Fatigue: Many felt that the Double Trouble Doc Ock/Kraven the Hunter arc ran too long.
To some, mainly newer readers, this can be applied to the entire series: Brian Bendis's Signature Style of decompressed storytelling, while new and groundbreaking when the series debuted (to the point of being copied and imitated by just about everyone in the following decade), has since come under greater scrutiny from the comic reading public, if not fallen out of favor completely. As such, many of the storylines can come off as slow or padded by modern standards.
Spider-Men, the crossover between the 616 & Ultimate universes to celebrate the fiftieth anniversary of Spider-Man's first appearance — is it a great idea, or yet another case of Quesada dropping the ball, given his previous comments on the matter of a 616/Ultimate universe crossover. Is it too soon to have Miles meet 616!Peter since the former is still finding his feet as a superhero, or just a wasted idea since it comes the year after Ultimate Peter was killed and shortly before 616!Peter is as well? The latter in particular, as it completely dropped the plotline going through the end of "Men".
Kitty Pryde became Peter Parker's girlfriend in and, after they broke up, remained a part of the cast and was fit into as many plotlines as possible. Brian Michael Bendis has gone on the record to state that he's always liked Kitty Pryde from back when he was a kid and that he enjoys using her... combine that with a statement he made about Peter "being him" and the conclusion to come to is pretty easy. Some don't mind the attention paid to her... but others do.
Ultimate Kingpin is this from a villain perspective since Brian Michael Bendis elevated him to second most prominent villain after Goblin, had him win unlikely victories (and a superpowered Peter Parker couldn't land a punch on him which 616!Marvel called BS on in an iconic moment in JMS' Spider-Man's Back in Black arc). Bendis is a huge fan of Daredevil fan (and later wrote Daredevil) and his ridiculously convoluted manner in which Kingpin escapes justice despite being caught on tape strangling a man beggars disbelief in terms of a Diabolus ex Machina.
Gwen Stacy. So much so they eventually brought her back and more or less said that even if she's a clone she's the same Gwen as before.
Jessica Drew is easily one of these, having minimal screen-time but a huge fanbase.
Miles' supporting cast is getting popular, such as Ganke and Rio Morales.
Foe Yay: During the "Return of the Green Goblin" arc, we get to look at things through Norman's eyes during a conversation with Spider-Man. The voices in his head tell him things like "kill him" "skin him" "burn him" and "kiss him".
Back in the early nineties, one of the most famous songs by Italian band 883note that now, by the way, is no more since its lead singer is now pursuing a solo career was titled "Hanno Ucciso L'Uomo Ragno", which is Italian for "They Killed Spider-Man". Fast-forward by twenty-years-or-so.
In "Cats and Queens", the focus of MJ's story was her wanting to run away from home so she and Peter could be married, with him saying he'll always be there for her. Also in the same arc, Black Cat tells him he'll have seven years bad luck. This was in 2004...
Similarly, every time the subject of sex came up between Peter and MJ, they resolve to "wait until they're older".
At July 2005's San Diego Comic Con, in response to the question the Ultimate & 616 universes crossing over, Joe Quesada stated that he'd rather close down one universe than have them cross over because it meant they were officially out of ideas. Fast forward to 2012, and Marvel announced that they will be having 616!Peter crossing over to the Ultimate universe to meet Miles.
Ho Yay: Apparently Miles and Ganke gave this off to Miles' parents...not that they mind. Doubles as Mistaken for Gay.
Jefferson [after talking with Miles about his relationship with Kate Bishop]: Good to hear. For a while there I thought you and the Gankster had a thing going. Miles: What?! Jefferson: Frankly, your mother thought that years before— Miles: Mom thought that Ganke and I were...together? Jefferson: Nothing wrong with— Miles: Ew.
A small detail, but in the 2004 "Hollywood" arc, when Peter fights Doc Ock on the set of a new Spider-Man movie, a black stuntman in a Spidey outfit hits Doc Ock with a camera. When he tells Spidey that he's just a stuntman, not the actor playing him, Peter says "I thought I got revamped there for a second..."
In one of the first issues, a photo can be seen that shows a young Peter with his aunt and uncle at Disney World. This was many years before Disney actually purchased the company.
It's the Same, Now It Sucks: The series at times reuses plotlines and ideas from the original even when they have become The Artifact. A good example is Ultimate Gwen Stacy. The original reason why 616!Gwen was fridged was precisely because she was a bland Love Interest and that it was only her death that made her interesting. Ultimate Gwen Stacy having a more interesting look and personality, and likewise not being Peter's Love Interest at the time of her death, and Mary-Jane being the love of Peter's life from the start, renders the entire purpose for her fridging non-existent. As such the arc where Carnage kills Gwen is more or less marking The Stations of the Canon and adding drama and tragedy to Peter's life, and of course when they returned Gwen back to life anyway, via a clone (who is both a clone and yet as good as the real thing), it made that entire issue pointless.
Magnificent Bastard: Kingpin, he makes Lex Luthor look like a chump. For example - he bought out the wrestling company that Spider-Man made his first few public appearances for prior to becoming a superhero, purely so that he could make money over Spider-Man's likeness & knowing that Spidey's choices were A) quit being Spider-Man, allowing his profile to fall & kill off the demand for Spidey merchandise so Fisk couldn't profit from him, but at the cost of being unable to stop his operations; B) publicly unmask to claim ownership of the Spider-Man likeness & stop Fisk from merchandising it, but making his loved ones targets for Kingpin; or C) let him get away with it. Fisk even points out that if Peter quits, he'll just hire a new Spider-Man to make sure that people still want to pay for Spidey merch.
The final issue of Fallout ends with Nick Fury confessing to MJ how he feels responsible for Peter's death. In the middle of it, he admits he had been "grooming" Peter to be a super-hero. Not the best choice of words, given the unpleasant other connotations that word has in the twenty-first century.
In the middle of his long rant at Miles and Spider-Woman, Roxxon randomly yells "childcare" for no readily apparent reason.
Seinfeld Is Unfunny: Upon its initial release, the mainstream universe Spider-Man was in the middle of a Dork Age following the end of The Clone Saga, and a back-to-basics style book like Ultimate Spider-Man seemed fresh and inviting to new readers(as a good jumping-on point) and longtime readers (who wanted a return to classic storytelling) alike. Fast-forward almost two decades and over 200 issues where the characters haven't left the teenage time bubble of The Oughties while most of its readership have grown up and new generations of teenagers find it a little dated. Many elements introduced in the book were later adapted in some form into the mainstream universe titles, while its family romance backstory involving Peter's Dad creating the Venom suit was adapted in the poorly received The Amazing Spider-Man Series which in turn tarnished its legacy further. Likewise, aside from some modernizations and changes, it didn't really succeed in entirely updating the characters and elements to a contemporary era.
Ship-to-Ship Combat: Who made a better girlfriend for Peter; Mary Jane, Gwen Stacy, or Kitty Pryde. Have a lot of fun with that conversation.
The main dislike is that Bendis took "teenage" Spider-Man to mean "incompetent" and that Ultimate Spider-Man gets unmasked all the time, not only to major villains like the Goblin but also minor random characters like Silver Sable. Apparently the fact that 616!Peter went through his original high school arc (which was a mere 28 issues by the way) with no one deciphering his secret and then with only the Goblin knowing it, was too much to handle. Likewise, Spider-Man was so competent that when Green Goblin finally unmasked him in OTL, he was shocked that Peter was Just a Kid since he was certain he was an Experienced Protagonist, the overall effect goes from Batman turning out to be as young as Robin, to Robin trying to be Batman and failing.
Lot of fans disliked the changes to villains. The Green Goblin becoming a giant goblin monster who can throw fireballs was a neat concept in theory but it in effect made Norman more of a Hulk or Captain America villain than a Spider-Man one, and also made him too similar to Curt Connors (i.e. scientist who turns evil by transformation). The popular villains in the Ultimate run were the ones who were the least changed (Doctor Octopus, Kingpin, Electro).
Played straight with the transition from Ultimate Spider-Man to Ultimate Comics: Spider-Man. The change of artist and shake up of status quo has resulted in a more Broken Base. The second transition to an entirely new main character was less so.
Having Spider-Man undergo training from the Ultimates to become a better hero was an interesting idea...that was introduced just before volume three. For what it's worth, that ended up being the basis of the otherwise unrelated cartoon. So presumably someone in development agreed.
Peter coming back from the dead, since nothing ever came of it, and the entire ultimate universe got blown up a few months later anyway. The idea of Peter and MJ eloping and going underground and presumably having crazy adventures on their own, has a lot of potential but now that's just gone.
Though in the latter two cases, they actually did come back.
Unnecessary Makeover: Mary Jane was on the receiving end of one via Liz Allen in one story, which involves wearing incredibly skimpy clothing and dying her hair black.Said arc wasn't very popular. MJ herself even hates it, and quickly ditches it the first chance she gets.
Carol Danvers qualifies over and over again. She refused to just put Norman down, instead, every single time she chose to keep him alive in a prison he's proven capable of breaking out of at will. This reaches critical mass at the start of The Death of Spider-Man - not just Norman, but five other dangerous superpowered criminals break out of the Triskelion, all of whom are enemies of Spider-Man, and the last time five of the six teamed up, it required the Ultimates to stop them. So she not only sends the Ultimates off to fight Nick Fury's Avengers to cover her own ass, but she doesn't even tell Spider-Man that six of his enemies have all escaped from incarceration, all so that she can keep the breakout a secret. And the kicker? Because she inadvertently caused the death of Spider-Man, this wound up being the straw that broke the camel's back and got her fired from her position as Director of S.H.I.E.L.D.
Eddie Brock Junior gets major points here. After being told by Peter that their fathers' life's work is actually dangerous in the extreme, and that Peter, a guy with superpowers, barely survived using it for a few hours at most, Eddie decides the best thing to do is get the other sample he had hidden, and stick his fingers in it. And as a result he ends up stuck in a living nightmare, hunted by a megacorp with an unrelenting hunger driving him to eat people.
Venom's wanted level you unlock post-game is clearly inspired by Grand Theft Auto's. However, unlike GTA, Venom's wanted level only has 5 stages to it rather than 6. And then Grand Theft Auto V did the exact same thing, with only five wanted levels.
Narm: Spidey's game over screen is pretty melodramatic, with the web-slinger exaggeratedly falling to his knees as the ashamed faces of his loved ones look on in the background. It becomes even more hilarious if you failed something as simple as catching up to the Rhino after you exposed his weakspot, making it seem as though Peter had absolutely failed everyone by not being able to stay close enough despite the villain only traveling to a parking lot not far from where they started.
Take That, Scrappy!: In the video game, Venom's tutorial presents you with your first task of absorbing people so that you don't lose health, your first target? A child holding a balloon. In Spider-Man 2, everyone hated the missions of helping kids who constantly lose their balloons.