What would be an interesting discussion is the possible change of the regular line-up of the X-Men.
*Xavier being away with Shi're Empire.
*Magneto is a temporary leader.
*Storm losing her powers, temporary.
*Bishop going back to the future. (Wasn't a regular member, and its still a question why he was back in the present anyway)
I like the concept of a rotating cast of temporary members that stick around for a while, serve a purpose, and moves on.
For a reminder of the regular members in the 90s comics -
*Iceman was only in 1 episode of the OG series, and it'd be interesting to see him return to the team for a while.
*Nightcrawler was only in 1 episode of the OG series, and had never been a member of the X-Men.
*Collossus was in 2 episodes. Never a member of the X-Men.
*Psylocke was in only a few episodes of Season 4, which I consider to be the series finales. She was merely a side-character, unfortunately.
*Archangel made several appearances throughout the entirety of the OG series. Never a regular member.
Perhaps Morph changing into Archangel, Collossus, & Psylocke were just cameos.
As for excuses for regular member absences, a famous arc for Wolverine in the 90s was when his adamantium was stripped out of his body... extremely painfully. He had perhaps one of the most interesting arcs for how he adapted to live without it.
I'd be fine with any excuse for Jubilee to have a long absence from the show.
Anyway, this is just me spitballing thoughts.