The adaptation of Secret Wars (1984) was originally going to feature a number of additional characters, most notably the entire X-Men roster note Only Storm made the final cut, the Hulk, and 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.) Likewise, the Hulk having a series on the competition UPN network forbade him from appearing; his role in the story ended up being given to the Lizard.
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 to prevent the Hobgoblin since toys were already being made, but he did rectify it by having Norman Osborn create the Hobgoblin's weapons instead of being the Hobgoblin. Some elements from Hobgoblin’s two-parter debut episode also imply that the script was originally written with Green Goblin in mind, especially the major plot point of Hobgoblin putting Aunt May in a coma and thus making Peter’s beef with him a lot more personal than with any prior supervillain (at that point), as well the ominous ending, where Hobgoblin flies off into the night sky while ranting, “Don’t forget me, Spider-Man. I’m not going to forget you”.
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.
Season 5 was going to feature an episode where Spider-Man teamed up with Ghost Rider to stop Baron Mordo and Mysterio (who had survived his apparent death in the previous season) from freeing Dormammu from his home dimension. The episode was never made because UPN was planning on making their own Ghost Rider series and Fox didn't want to promote a character on a rival channel.
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. Interestingly, Beetle did appear in tie-in merchandise for the series, including the video game and the comic book adaptation The Adventures of Spider-Man (he also made a brief appearance in season 2 of Iron Man: The Animated Series during the "Armor Wars" two-parter).
Norman Osborn would have returned from limbo and reclaim the identity of the Green Goblin from his son Harry.
Because of The Incredible Hulk (1996) 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.
