***

Yep. A persistent problem in superhero comics, not just an X-MEN problem. I think of all the Spider-Man supporting cast members who became super-people:

John Jameson (Man-Wolf)

Harry Osborn (Green Goblin II)

Ned Leeds (Hobgoblin, sort of -- he was brainwashed)

Liz Allen (stepsister of the Molten Man -- not the same thing, I know, but too coincidental)

Flash Thompson (as mentioned, he became Agent Venom)

I may be missing others. 

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X-Treme X-Men was just Claremont having Tessa/Sage Mary Sue (a term I really dislike, so for me to use it tells you how badly Claremont was writing Tessa) all over the place, while at least the first half of Whedon’s run was the only thing that had felt like X-Men in a long time, so Quesada made the right call in both instances, no matter his reasoning. 

Another thing that bothers me with the X-Men in the last few decades, and Hickman is using these characters, is that too many former enemies are becoming X-Men. Beyond Rogue and Magneto, we've seen Emma Frost, Sabretooth, Mystique, and Juggernaut all become X-Men. As the X-Men now seem to have moved beyond being a team of heroes, Professor Xavier has forgiven all the murders and acts of terror that those characters have committed. Rogue was a character without much of a history so that worked as far as reforming the character goes and I'll admit I loved Magneto changing his ways back then but it seems writers don't want to write evil mutants any more.

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Yes, he was using a character to serve a story that he wanted to tell instead of telling a story that served the characters. Also see his FF run which at times seemed like leftover EXCALIBUR plots featuring Roma. 

" at least the first half of Whedon’s run was the only thing that had felt like X-Men in a long time"

I agree felt more like a classic X-Men run. It helped that he had Cyclops, Wolverine, Kitty Pryde, and was allowed to resurrect Colossus. He was able to get Kitty even though Claryemont wanted her and he was able to ignore Quesada's "Dead is Dead" policy even though Grant Morrison couldn't have Colossus. It was almst a cover band version of the stories that Claremont/Cockrum/JB/Smith/JR jr. did. 

So we're left with "cover versions", Marc Guggenheim and Matthew Rosenberg were the most recent at those attempts and those weren't bad comics but they felt like "Hey I'm writing these guys like Chris Claremont did" or we allow superstar writers blow everything up. Grant Morrison's run as the main book felt like his main goal was to break up Jean and Scott and make Scott and Emma Frost lovers. No costumes and Mutants were a culture of their own was probably as much editorial as it was Morrison. But the comic press (and Marvel) have us believe that run is one of the greatest of all the runs. And if a person feels that way, I certainly wouldn't say they're wrong because opinions are what they are but I don't hold that run in high regard. Hickman's run is being heralded the same way and in my mind it's because, like Grant Morrison, the writer is more important than what they do with the characters. Brubaker was able to turn Xavier into a manipulator worse than some of the villains they'd fought. I checked out after that so I'm not sure who was behind the Utopia stuff and slowing turning Cyclops into a terrorist. I blame Axel Alonso since he was always talking about Cyclops being his favorite character at the time. Hickman is now telling his story and inserting the X-Men into whatever he's trying to tell.

***

Not to get too deep in the weeds, but after two readings of the comic my understanding is that yours & Chris's Uncanny run happened only in one timeline -- which Moira was living for the first time (and thus could be surprised by new developments). 

When she was reborn again after that, she made different choices which led to a all-new, all-different "reality."