Quesada felt their were too many mutants, and that it was undermining the whole point of the X-Men.
Brian Michael Bendis wanted to put Wolverine and Spiderman in the Avengers (and his faves Luke Cage and Jessica Jones), while Quesada wanted to reduce the mutant numbers. Bendis (and indeed other writers like Millar and Hickman) regarded characters like Wanda, Vision, Clint, and Scott Lang (Bendis tried to kill him off even before Disassembled) as "lame" (ironic given the MCU has made those characters popular again).
John Byrne trashed Wanda in order to trash Vision back in the 80s (by making her crazy, he effectively was saying she was crazy to see Vision as a person), then Dan Abnett and Kurt Busiek fixed the damage...then Bendis decided to repeat what Byrne did (it being the only Wanda story he knew), ignoring all of Kurt Busiek's work in defining Wanda's powers.
Bendis made Wanda disappear from comics for nearly a decade, an exile that only really ended due to Joss Whedon pushing her into the MCU.
One of the interesting things about MCU Vision is that he appears to be a pretty big repudiation of the way John Byrne (it's him who called Vision a "toaster") and most modern Marvel writers (Tom King excepted) view Vision.