Creator Backlash: While the Hobgoblin was popular in both the comics and the show, John Semperhated the character (both then and now) and only used him because toys were being made based on decisions made by his predecessor.
Some say the writers weren't allowed to use the words death, die, or kill; hence, when Peter found out Uncle Ben had been killed, it was shown as a police officer shaking his head and saying "I'm sorry, kid. The guy was armed." Also, realistic guns were out, so even petty thieves were armed with futuristic lasers.
Oddly, the word "kill" was actually used more than once, when referring to "killing" a news story, and briefly when Spider-Man asks why Black Cat doesn't want to kill him if she worked for the Kingpin. Also, when Flash complains to his girlfriend about how Michael Morbius almost "killed" him. Mac Gargan (who would later become the Scorpion) said he'd "kill for the chance" to get back at Spider-Man. Given the abundance of assumptions online that several specific creative choices in the show were down to censorship, it's possible this is yet another common misconception, so take this with a pinch of salt.
A case of executive meddling having an outright odd effect was in the character of Morbius, a vampire. Allegedly, the writers weren't allowed to show him sucking blood through his fangs, so he apparently has fangs for no reason, as he instead drains plasma through suckers in his hands. The suckers were so squicktastic that they made the character even creepier, whereas his declarations of "I hunger for PLASMA!" were often Narm. Interestingly enough, the Swedish translator had him hungering for blood plasma.
Another example is Carnage. In the comics, he was a mass-murdering psychopath, but in the series he wasn't allowed to kill anyone — instead he sucked out their "essence" through his hands, which was restored to his victims after he was sucked into a portal. In the scene where he acquires the symbiote he attacks some prison guards; he picks one up and makes some knives with his fingers but instead it shows him busting through a wall. In all fairness to Fox, the NYPD's description of Cletus Cassidy implied his psychopathic tendencies, not to mention his mannerisms and laughter were still pretty creepy in their own right (especially the laughter). So while Carnage could not kill anyone, the censorship didn't stifle his sadistic personality.
It's worth noting that there's a common misconception that Spider-Man wasn't allowed to punch anyone, as it would make the show too violent. This is very much not the case, as the showrunner, John Semper Jr., often reiterates online; the lack of punching was a deliberate creative decision to make the fights more creative, and visually interesting.
One positive effect occurred when the writers were forced to introduce the Hobgoblin in season one rather than the Green Goblin, to match the toys that had been ordered. This allowed Hobgoblin to become an engaging character in his own right and a precursor to the more dangerous Green Goblin.
The Punisher had to undergo some censorship, one could say(Though whether it was mandated by executives, or decided on in advance by the showrunner is unknown). He was purely non-lethal, though this is mentioned in-show as a deliberate thing he's doing as a one-off for his effort in chasing Spider-Man, with it being a "Legit job" for him to do without killing anybody, for once. So, pretty clever handling of that.
The telling of The Punisher's origin (for those unaware, the brutal shooting of his wife and young children which obviously couldn't be shown) was incredibly effective. The only visual was a kite flying in the sky and at the sound of gunshots fell to the ground, landing in a puddle and forming the classic skull as it became soaked in water.
Why Sandman never appeared and Electro was an altered character. When the series started, James Cameron's movie was going to feature the two as villains (though with heavy tweaking), so the writing team were told not do use either. However, by the end of the show's run, it looked like the James Cameron movie wasn't going to happen, so the showrunner snuck Electro in as the Big Bad of one of the story arcs, and got away with it.
There were originally plans to have Ghost Rider in an episode, but the episode was scrapped due to Ghost Rider having a series planned for UPN, which didn't happen.
Allegedly, a full script was written, and given out to backers of the showrunner's Indie Go Go for a series he was trying to get off the ground in 2016.
Another UPN-related character embargo happened because of The Incredible Hulk airing on that network. Because of this, the Hulk is only mentioned a few times in the series and couldn't be used in the show's Secret Wars (1984) adaptation, which replaced him with the Lizard.
It may be due to the fact that the notion of Unlimited being a sequel turned out to be a case of Critical Research Failure. Shortly after Spider-Verse happened, fans asked the people behind both shows if they were related and they responded that they were intended to be separate continuities, meaning that this Spider-Man never appeared let alone died in Spider-Verse.
Keep Circulatingthe Tapes: For whatever reason, the series has never had a full DVD release in the United States. A full DVD set of the series was released in Europe however and the series has streamed on Netflix and other sites.
Marth Debuted in "Smash Bros.": If it wasn't the movie, most familiar with Blade were first introduced to him in this series. Heck, it's likely because of this series that film was possibly more successful due to people remembering him here.
Missing Episode: Following the 9/11 attacks, ABC Family pulled "Shriek of the Vulture" and "The Final Nightmare" (both of which featured a burning skyscraper) from the rerun schedule. These two episodes concluded the Neogenic Nightmare arc and led into Season 3's "Doctor Strange", so you can imagine how displeased fans were. It wasn't until the end of 2007, though, that this changed. Toon Disney aired the two episodes as a part of an all-series New Year's Eve/Day marathon. As long as the show has been airing, the two episodes have been rerun regularly ever since.
Within the '90s Marvel cartoons, War Machine fall under this, with the character going back to his first voice on Iron Man James Avery.
While The Other Darrin within this series, similarly during the "Secret Wars" arc, Storm plays around with this as she went from her second X-Men voice actress Alison Sealy-Smith (who voiced the character during the X-Men's guest appearance) to her original voice actress, Iona Morris.
War Machine reverses this, going back to his voice actor in season 1 of Iron Man, James Avery.
Storm also reverses this and plays this straight: During the guest appearance of the X-Men, Alison Sealy-Smith (who was the second voice of the character on X-Men) reprised the role, but when the character appears solo in the "Secret War" arc, she was reprised by her first actor from X-Men, Iona Morris.
Promoted Fanboy: Armando Coria, the Mexican voice actor who voiced Spider-Man in the Mexican dub of the series, is a hardcore fan of Spider-Man since childhood.
Recycled Script: "The Spot" and "Goblin War" come one after another, and they both have the exact same plot beats. A villain is using a portal device to commit robberies. The Kingpin gets involved somehow. Felicia has a scene where she flirts with Spider-Man despite being engaged, to which he brushes her off, leaving her sad. Harry has a scene where he acts petulant toward Peter about how he "stole" Mary Jane from him. Spider-Man ends up at Crime Central where the Kingpin almost squeezes him to death. Of the two episodes, "Goblin War" is the more important due to the re-emergence of the Green Goblin and the Hobgoblin's identity being revealed, so one could almost skip "The Spot" entirely and not miss much.
Screwed by the Network: Sort of...it's a bit complicated. The show was always intended to have 65 episodes as was tradition at the time but it was popular enough it could have received more episodes but the head of development for Fox Kids hated Avi Arad, who was the producer for the show. Story Editor and showrunner John Semper has gone on record in saying he ended the show in a way he considered to be definitive enough that it was a satisfying ending, but that if it was renewed for more, there was still room for the story to go further.
Unintentional Period Piece: Besides the odd reference to 90s pop culture, the Man-Spider arc blatantly dates itself to pre-2001 when it turns out Man-Spider's lair is under the World Trade Centre parking garage.
The adaptation of Secret Wars (1984) was originally going to feature a number of additional characters, most notably Mister Sinister. These were later scrapped for numerous reasons — namely costs since Sinister's voice actor, Chris Britton, is Canadian-based (the cast of the X-Men series had previously been flown to LA from Canada for their appearance in the crossover, which proved expensive. Storm got to appear because she's a case of The Other Darrin, and her former voice actress was in LA.) And The Lizard's spot was originally made for the Hulk, but he had a series on UPN, so he couldn't be there.
The first showrunner that John Semper replaced before actual production on the show started intended for Norman Osborn to become The Hobgoblin,which likely meant the Green Goblin never would have shown up! This was probably due to the Green Goblin being dead at the time the show started. When Semper came in it was too late too prevent the Hobgoblin since toys were already being made but he did rectify it by having Norman Osborn create the Hobgoblins weapons instead of being the Hobgoblin.
As stated above in Executive Meddling, the Sandman never appeared on the show and Electro's incarnation was drastically different from his comics counterpart because of James Cameron's attempt at making a Spider-Man movie with Sandman and Electro as the villains. One can only guess how things would have been if the Sandman got to appear on the show and if Electro's origin and identity stayed true to the comics.
Proposed ideas for the unproduced sixth season:
The Mary-Jane Watson subplot would have been resolved by having Spider-Man find her in 19th century England and bringing her home with Madame Webb's help. The episode also would've revealed that Carnage was Jack the Ripper.
The villains the Beetle, Puma, and the Rose were considered to appear in the series.
Norman Osborn would have returned from limbo and reclaim the identity of the Green Goblin from his son Harry.
Because of The Incredible Hulk ending its run at the time, there was a chance that the Hulk might have finally made a guest appearance instead of just being mentioned.
John Semper thought about doing an episode spoofing Spider-Man and His Amazing Friends that would've had Frank Welker and Kathy Garver reprise their roles as Iceman and Firestar and would've ended with the three heroes going their separate ways after agreeing that they're better off not working as a team.