I adored X-Treme X-Men, especially in regards to Claremont's use of Storm. She was spectacular. But the fact remains that X-Treme was the satellite book orbiting around Morrison's New X-Men. That is what defined the X-Men for the 21st century.
Given that Morrison's intention was to make Storm start a relationship with Cyclops instead of Emma, I am completely happy Claremont intercepted her, but in the long term, that did come at the cost of Storm's relevance to the 21st century X-Men.
Marrying Storm off to BP was another step in the wrong direction, but she was already on shaky ground due to missing Morrison's run. Like it or not(and certainly the fandom is divided), Morrison created Weapon Plus, the Cuckoos, Fantomex, elevated Emma, created Quentin Quire, Glob, Xorn, Cassandra Nova, made the X-Mansion into an actual school with dozens-hundreds of random students, killed Jean, made mutants into a huge population and then killed a huge chunk of them, destroyed Genosha, etc, etc, all of which are storypoints/characters still in play to this day. Storm not being in the center of that has had huge consequences. And you can easily see a lot of younger/newer X-fans straight up don't like Storm(and it's almost fair, because her greatest stories were decades ago).