It was more that JMS's run had done a LOT with Peter's character and relationships (one of the arcs was "Evolve or Die" and really emphasized a "you can't keep your characters stagnant for thirty years" theme that was the focus of the run) and the Mephisto thing also undid all of that for...amazingly stupid reasons. It wasn't just that they broke them up (after JMS did a nice job of convincingly building back up their relationship) or that it flew in the face of the "choices have consequences" them from the rest of the comic, it was that it actually allowed PETER PARKER, not Spiderman to be the center of the story and his relationships. Other superheroes reacted differently to Peter with the mask off, Peter got to be a positive influence on his community as a teacher and MJ and Aunt May's lives would intersect and be affected by his life as a superhero. And all that went away instantly. (It's abundantly clear that if you don't know there's an insecure nerd under the mask, Spiderman's wisecracks are obnoxious.) There's a great story from Fraction's FF where Peter volunteers to teach a class...but without knowledge of his teaching career during JMS's run or you know and with Spiderman's "Ryan Reynolds with less confidence" public persona, Reed doesn't think he's qualified.
Okay, stepping off my "One More Day made me stop reading Spiderman" soapbox, but that kind of editorial BS led to JMS leaving Marvel which derailed his very good Thor run.
