These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Badass Decay: Several villains. The Lizard in particular gets this bad past his initial appearance.
Broken Base: The quality of episodes after the first season. Some fans think that the show grew the beard after the first season with its story arcs, Character Development, focus on Peter's personal life, others think that the show declined in quality, citing bad animation, constantly recycled footage, the overuse of the Kingpin, Morbius or Madame Web and more space and vampire stories.
Christopher Daniel Barnes as Spider-Man. Many fans think that he is the definitive voice for Spider-Man, like Kevin Conroy is the definitive voice for Batman. But there are fans who think that Barnes was way too melodramatic as Spidey and his voice didn't fit Spidey at all.
Cletus Kasady, aka Carnage, is introduced as an Ax-Crazy lunatic willing to use a bomb to kill himself and everyone within a 200 meter radius just for giggles. After entering into the service of the Dimension Lord Dormammu and bonding with the offspring of Eddie Brock's symbiote, Kasady uses his newfound power and connections to become an even worse menace. Unlike Eddie who, when bonded with his symbiote, creates a combined persona called Venom, Cletus is so psychotic that he still remains completely aware and in control after bonding with his symbiote. First helping Venom steal an interdimensional probe, Kasady quickly displays contempt towards his "dad's" softness and proves himself willing to kill Venom on the flimsiest of pretexts. Kasady would later go on to steal the souls of numerous innocent people in order to summon Dormammu and herald The End of the World as We Know It. Once Spider-Man defeats him by letting him be sucked into Dormammu's home dimension, Kasady attempts to grab Eddie Brock's Love Interest, Dr. Ashley Kafka, to take her with him. He's only thwarted by Eddie sacrificing himself instead. Rampantly homicidal and needlessly sadistic, Kasady was a far cry from the usual Spider-Man villain, doing evil solely for the carnage it unleashed on the world.
Herbert Landon is a Mad Scientist, the Evil Former Friend of Hank McCoy, and a genocidal Smug Snake driven solely by hatred. A rabid anti-mutant extremist, Landon created a formula that destroyed mutant cells and killed any mutant exposed to it. His endgame was to market this formula to the public as a cure for mutants only to instead use it to wipe them all out. The first person Landon attempted to test out this formula on is his "old friend," Hank. Thwarted in this endeavor, Landon would go on to become The Dragon to the Kingpin, and performed various unsavory deeds such as forcibly converting Alistair Smythe into a cyborg slave and testing out a Super SoldierSuper Serum by using Felicia Hardy as a guinea pig.
First Installment Wins: There are fans who see the first season of the show as the one with the most memorable and well-written episodes, like "The Night Of The Lizard" and "The Alien Costume Saga", and with the best animation in the entire series. The following season are more divisive.
Hilarious in Hindsight: In the first episode Spidey complains about why he has to crawl around sewers and can't land an easier superhero gig with the Avengers. He also complains about not being "a galaxy hopping superhero," which he essentially becomes in the final episodes.
In episode 48 "The Vampire Queen" Whistler wonders why all the girls go after vampires and if it has something to do with the fangs. Maaany years before Twilight.
Then there's pre-vampire Morbius, who looks and sounds kind of like Tommy Wiseau.
Jerkass Woobie: J.Jonah Jameson's distrust and dislike of Spidey make much more sense when we learn that his wife was killed by a masked gunman. Alistair Smythe arguably qualifies for this trope, along with Morbius.
Also, the scene where Kingpin's wife leaves him is surprisingly sad and is the one time the Kingpin shows actual remorse for his actions.
You could make a case for all of the antagonists on the chance that they pull an Enemy Mine with Peter.
Narm: The epic Executive Meddling the show faced to make it more kid-friendly. Especially odd is their treatment of Morbius; any kid knows what vampires do, so who exactly did they think they were protecting?
Hydro-Man. Everything about Hydro-Man. He's an obsessive Stalker with a Crush, and he has superpowers that allow him to get around/into practically anywhere to find you (if you're Mary-Jane Watson) and make him virtually tireless and exceedingly hard to slow down, or even hurt.
The cab drivers from the episode "Attack of the Octobot. Big time, especially Mousie. It's mostly due to their annoying voices. Tina from episode the same episode and "Make a Wish" qualifies to lesser extent.
Take That, Scrappy!: Spidey's tirade against Madame Web matched what many viewers felt about her.
Spider-Man: I am sick of you... and your riddles. And your lessons! And your SUPREME ARROGANCE! Don't you ever, EVER enter my life again! Do you hear me? DO YOU HEAR ME!?
And she did, until the "Secret Wars" episodes. Which she says she foretold about before leaving.
Tear Jerker: The death of the Mary Jane clone was positively gut wrenching.
Villain Decay: Many of the villains within the course of the show suffered this. Most glaring would be:
Dr Octopus, who became a mere flunky for the Kingpin, even giving up on his plans to become The Starscream shortly after the time he got defeated by a child.
Hobgoblin, who was revealed to be nothing more than a petty crook and a wuss in his last appearance.
And Alistair Smythe, who Took a Level in Badass by becoming a mutant and leaving the Kingpin's services only to end up becoming a flunky for Silvermane in an even less important position than he was as the Kingpin's lackey.
What an Idiot: In "Day of the Chameleon," none of the SHIELD agents present noticed that "Nick Fury"'s eye-patch was on the wrong eye, despite being right in front of them. Spidey was briefly fooled, too, but he noticed after mere seconds and despite being farther away.
The Woobie: True to the comics, the sheer amount of crap poor Spidey gets put through over the course of this show, particularly from the second season onwards, is unbelievable.
Iron Woobie: The Scarlet Spider. He's been through all the same trauma that Spider-Carnage has, but somehow came out okay.