Following the abrupt departures of Joe Kelly and Steven T. Seagle in 1997, X-Men and Uncanny X-Men spent several years with a revolving door of creative teams.
The Astonishing X-Men ongoing series took full four years to complete a 25-issue storyline. As a result, Shadowcat being Put on a Bus was spoiled by Messiah Complex: since its events couldn't take place before it, Kitty was nowhere in sight. The series is notoriously hard to fit into Marvel continuity, as it appears to take place over at most a few weeks, but the second arc is set prior to House of M (Xavier and Magneto are hanging out on the ruined Genosha), the third is set after Secret War (Maria Hill has taken over from Nick Fury as director of SHIELD), and the final arc includes a dialogue reference to Civil War having happened! The series was first written by Joss Whedon and then Warren Ellis continued the trend. The reason is the same.
Un-Canceled: The original X-Men title was canceled after seven years of horrible sales and no popularity (it was revived nine months later, but only published reprints of earlier issues). It was basically seen as a poor-man's version of the Fantastic Four. Then it was rebooted with all new characters like Nightcrawler, Storm, and Colossus, along with minor Hulk antagonist Wolverine. Under the skilled writing of Chris Claremont, it became Marvel's flagship title throughout the '80s and '90s.
During the battle against the Shi'ar Imperial Guard, Wolverine's costume is destroyed, whereupon he takes that of his opponent Fang for himself. Cockrum intended him to keep it, but John Byrne found it ugly, so he had Logan quickly peel it off as soon as he got home.
Madelyn Pryor was originally intended to be just as she appeared - a woman who looked exactly like Jean, but nothing more. However, when plans were started to resurrect Jean to reform the Original X-Men for the 25th anniversary of the title, a major problem presented itself - Scott and Maddy had married and were happy. That's when the Summers marriage fell apart. Hence the twist that she was a clone engineered by Mister Sinister, her becoming the Goblyn Queen and her death during Inferno.
Mister Sinister;s origin was originally very different: he was a young rival of Cyclops who couldn't age. By the time Cyclops was an adult, Kid Sinister was still stuck as an 8-year-old (physically and mentally), and he used his mutant powers to change his appearance into that of a gaudy, over-the-top supervillain: an 8-year-old's vision of a cool supervillain. When considering that origin, Mr. Sinister's corny appearance, unimpressive name, and stereotypical supervillain demeanor actually make sense. It also explains his minions: The Nasty Boys (a name an 8-year-old would be far more likely to pick than a mad geneticist) earn their name by being filthy ultra-slobs, living in conditions akin to the X-Men: Evolution version of the Brotherhood. In other words, they never take baths or clean their space - part of an 8-year-old's idea of perfect freedom.
Sauron was originally supposed to be a vampire. Also, Claremont considered bringing him into the X-Men full-time as their resident doctor in the 1980s.
The story with the X-Men facing Krakoa in Giant-Size X-Men #1 (May, 1975) is familiar. But it was only the second concept for the reintroduction of the team to readers. The original one was rejected. According to Dave Cockrum, the original story would feature figures from Aztec Mythology. "It was something to do with sending the new team down to South America to rescue the old X-Men and finding a whole bunch of Aztec gods walking around and raising hell and having to combat the Aztec gods who would wind up to be the original X-Men dressed as Aztec gods." Cockrum disliked the idea and convinced writer Len Wein to dismiss it and start working on another one.
One early version of the story in Giant-Size X-Men #1 would have the original team be in no real danger. Instead of an actual mission, the entire dangerous situation would turn out to be an elaborate entrance exam. Testing potential X-Men for the proper skills to actually join the team. And there would be those who flunked the test and be rejected. The obvious candidates for Len Wein and Dave Cockrum were two already established characters: Banshee and Sunfire. Originally they were supposed to be the only ones. Then the creators decided to also have one of the new characters fail. Choosing Thunderbird, whose flaw of being anti-social would make him unsuitable. The duo of creators started having second thoughts about letting Banshee and Thunderbird go, which resulted in them scrapping the idea of the exam.
Some of the new X-Men were loosely based on character concepts Cockrum had unsuccessfully pitched to DC earlier (as "The Outsiders"). Most prominently, that pitch included an Anti-Hero called Nightcrawler who ultimately got to keep both his name and appearance.
Edited for Syndication: A few episodes had retakes and were rebroadcast with different and corrected scenes. "Night of the Sentinels Pt. I" had three versions: 10/31/92, 1/9/93, and 4/3/93. "Night of the Sentinels Pt. II" had three versions: 11/7/92, 1/9/93, and 4/10/93. Both episodes aired as a one-hour special on 1/9/93. "Enter Magneto" had two versions: 11/27/92 and 1/16/93. "Slave Island" had two versions, the first on 2/13/93 did not have the cliffhanger ending with the X-Mansion wrecked.
Fake American: Most American characters such as Cyclops, Jean Grey, or Jubilee are voiced by Canadian actors. Professor X is voiced by an Englishman, and Rogue (who is meant to be from Louisiana) is voiced by Lenore Zann, an Australian raised in Canada who spent time in LA before moving back to Canada.
Fan Nickname: Many of Jean Grey's screams n moans in the show have been referred to by fans as "Jean gasms".
God Does Not Own This World: Stan Lee was not creatively active with Marvel comics at the time the series was being produced so his involvement wasn't particularly big on the series. He gave some producers notes on the first thirteen episodes.
Master Mold gets a new voice actor in season 4, who sounds completely different. Justified as it's a new model of Master Mold made after the original was destroyed.
The Other Marty: For Mister Sinister's cameo appearance at the end of "The Final Decision," an actor was directed to read the line in a campy fashion. The writers would later develop Sinister as a more serious villain. After Christopher Britton was hired to voice the character, he re-recorded Sinister's original cameo. The re-recorded cameo appeared in various reruns for years, though the DVD release would feature the original version.
This also applies to Gladiator in his appearances, with his lines originally recorded by an unknown (and uncredited) actor before replacing him with Richard Epcar (who also went uncredited) for TV airings and reruns. Similar to the Mister Sinister example above, the DVD release features the original performance.
Out of Order: Some episodes that were intended for season 4 were pushed up to the third season. In turn, some season 3 episodes were pushed back - most ridiculously the episode "No Mutant Is An Island" which is supposed to take place during Jean's death between the Phoenix Saga and the Dark Phoenix Saga.
"The Unstoppable Juggernaut" originally had to be aired after "The Cure" and "Come the Apocalypse" due to animation problems. The preceding episode "Slave Island" needed to have its ending tweaked to show the mansion intact, but the change still caused continuity hiccups (such as Xavier's being away and the mansion needed to be rebuilt). This was all cleaned up in reruns.
Postscript Season: Word of God states the "Beyond Good and Evil" four-parter was originally intended to be the Grand Finale. A renewal order led to more episodes being produced before the final end with "Graduation Day."
Troubled Production: "No Mutant is an Island," "Longshot," and "A Deal with the Devil" had to be pushed back two years due to severe animation problems. Production was lucky, though, that other episodes were ready to go and fill out the slots.
An even more severe case happened with the "Night of the Sentinels" two-part pilot, to the point where the animators refused to fix them until Fox threatened to sever the contract.
Unfinished Episode: While 76 episodes were produced, there remains one script that never made it into active production. It was called "Bring Me Charles Xavier," and would've brought back Colossus, Illyana, Omega Red and Darkstar for a "hard-edged" story set in Russia. The script ultimately went unproduced after multiple note-givers raised concerns about the premise of the story.
The X-Man killed in the pilot episode was originally intended to be Thunderbird, which was meant as a nod to the character's death in issue #95 of the original comic. However, someone up top understandably thought that introducing a Native American superhero just to kill him off in the first episode had some Unfortunate Implications, so the creators replaced him with Changeling (renamed "Morph").
During the earliest production meetings, Professor Xavier, Jean Grey and Beast were not planned to appear in the show. The writers fought for their inclusion, arguing that they had important roles in the X-Men mythos.
As mentioned above, "Beyond Good and Evil" was meant to be the show's Grand Finale. Had it not been renewed for additional episodes, the series would've ended with Archangel, Psylocke, Bishop and Shard officially becoming members of the X-Men.
Conversely, had the series been renewed after "Graduation Day," Season 6 would've opened with a Time Skip showing the X-Men having to function without Professor Xavier. Much of the season would've featured the X-Men having adventures in space after receiving a distress call from the Shi'ar Empire.
For the second season, plans were made to have Archangel to be added to the team, but ultimately those plans were scrapped.
In the late 90s, Fox Kids was suffering from falling ratings and was looking for big events. Will Meugniot proposed an animated crossover between the X-Men and the Mighty Morphin' Power Rangers. It got as far as conceptual art before being scrapped; according to Meugniot this was because one property would be too successful than the other.
What Could Have Been: Multiple X-Men attractions were proposed for Universal Orlando's Islands of Adventure park during its development phase in the early/mid 90's. The first one would've had guests venturing inside of the Cerebro chamber and witnessing a big battle between the X-Men and Magneto's forces. The attraction would have utilized a moving theater that would've been surrounded by a giant 3D dome screen. The second proposal, which almost made it into the park, would have been an interactive dark ride where guests would be able to shoot at targets and score points. This fell through due to the extreme budget cuts the park received as a result of The Amazing Adventures of Spider-Man and Jurassic Park River Adventure going heavily over-budget. The third and final proposal was a stunt show, which too ended up being a victim of further budget cuts. An X-Men ride did finally come to park in 2000, though in the form of a small teacup ride called Storm Force Accelatron.