Marvel was really bad with female characters in the 2000s. It wasn't just the X-Women misused because they used Wanda as a plot device to break up the Avengers by making her go crazy and then throwing her into character limbo for years. Wasp was killed off at the end of Secret Invasion. MJ got written out after her marriage to Spider-Man was literally sold to the devil. Like if Marvel's most popular character's wife isn't safe from having her marriage erased from existence, no Marvel marriage is safe lol. I guess Storm got off better in that sense. Elektra had a movie come out but even then her character was killed off and revealed to be a Skrull.
I've always seen Storm as the one true leader of the X-Men (thank you Claremont for that) so this idea that she'd just be completely useless didn't sit well with me at all. It really was the Dark Ages lol. Rogue and Psylocke were lucky that they had writers who cared enough about them to invest in them in spin-off books safe from Cyclops and his cabal of villains. Storm had no such writer willing to protect her. I think Claremont had been taken off enough X-books by then that he lost his clout and wasn't allowed to write her once she got married and was no longer considered to be under the X-Office.
The sad thing is that it could have been way worse for Storm. Morrison originally wanted Cyclops and Storm to have an affair! Like even ignoring the fact that this man is Storm's best friend/sister's husband, the real truth of the matter is that Storm is too good for Cyclops anyday. She would never sully herself with the likes of him but Morrison actually wanted them to be a thing. That got scrapped luckily but in The Rise and Fall of the Shi'ar Empire, which was used to keep Havok, Polaris, and Rachel in space for years, the original plan was for Storm to be in this storyline. Polaris was a replacement for Storm because Storm had just been married off to Black Panther so she was considered off-limits by the X-Office at this point. All that makes me think is that because Marvel was already looking for a reason to write off Storm, that she could easily have been the one lost in space for years.