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 would be quite problematic, so the creators replaced him with Changeling (renamed "Morph").
Even more, Morph's death was going to be permanent but fan outcry resulted in him being brought Back from the Dead in season two.
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 under Post-Script Season of the trivia page, "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. However, the X-Men '97 revival would later pick up this plotline.
One of the episodes planned for the scrapped sixth season would've centered Colossus and his sister Illyana in a Darker and Edgier story set in Russia that would mark the return of Omega Red. It was ultimately rejected due to the production staff's concern about its premise and subject matter.
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.
According the show's art book, released in October 2020, Lawrence Bayne (Cable) auditioned for the role of Wolverine, but knew Cal Dodd was the better pick. They've remained good friends, though.
Stan Lee originally wanted to appear in a live-action introductory segment in front of each episode, but the creators feared that this would make the show seem too juvenile. Lee would eventually go on to film similar segments for Fantastic Four: The Animated Series and Iron Man: The Animated Series two years later.
before being scrapped; according to Meugniot this was because one property would be too successful than the other.