After "The Phoenix Saga" aired, the remaining episodes that aired were not in the correct continuity order. Because the bulk of episodes were being animated with many different studios, the writers decided not to continue with linear storylines like the first two seasons, as many would likely air as soon as they became available. Continuity problems became so bad that episode 3.8 "No Mutant is an Island" and episode 3.10 "Longshot" did not air for two years after they should have, thanks to animation quality issues. "No Mutant is an Island" was *supposed* to explain Jean Grey's return, setting up the Dark Phoenix Saga.
Due to late development for the first season, episode 1.08 "The Unstoppable Juggernaut" aired after episode 1.09 "The Cure" and episode 1.10 "Come the Apocalypse" during the first run. Because of this, a quick animation fix with re-edited footage was created for the original airing of episode 1.09 "Slave Island", showing the X-Men returning home to the Mansion and the Blackbird landing.
Sidney Iwanter, an executive at Fox, originally planned on "ending" the series with a big bang ("Beyond Good and Evil - parts 1-4"). We even had planned to have characters leaving the team at the conclusion, but at the last minute Fox asked for more episodes. Unfortunately, at the time Marvel was filing for bankruptcy and could not afford to produce more episodes, so Saban funded them directly. This explains why the last six episodes looked different than the previous 70. So the show officially "ended" things again with "Graduation Day."
Fox initially had a lot of resistance to the cartoon series before it became a success. They felt that the target audiences, kids under 10, wouldn't be interested in a romantic love triangle between Cyclops, Jean, and Wolverine. They also thought kids wouldn't keep up with a show that was serialized.
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
After the box office success of X-Men in the summer of 2000, Fox briefly aired reruns of the cartoon on weekday afternoons (at first they only broadcast episodes that primarily featured content in the movie, but later the series was aired in proper order).
The series artwork and X-Men roster were based on comic book artist Jim Lee's "X-Men" comics. Around the time of the series production, Lee was working on the comic series "X-Men: Legacy" (then called simply "X-Men"), which was ranked by the Guinness Records as the best-selling comic of all time.