As for me, I will always say that the launch of X-Factor was where the rot in the mutant books set in. I had fewer problems than most with Madelyne Pryor than a lot of other readers, but then right from the start she seemed to be distinct enough in looks and personality to me to be considered a person in her own right.(1) And the revelation that she was Jean's clone did nothing to alter that, because I belong to the faction "Clone Lives Should Matter in Fiction".
Unlikely coincidences are what the X-Men have been built on for ages(2), so I could live with that, especially as in the storyline that introduced her a lot of these coincidences seemed to have been influenced by Mastermind's doings. I liked Madelyne well enough not to wish her dead or written out of the series. To be honest, with Rachel assuming the mantle of the Phoenix and Madelyne as Scott's wife, I saw no reason to bring Jean Grey back. All that slightly bothered me about Madelyne were a few loose ends, but loose ends is what Chris Claremont's writing is all about.
And there's no saying that a satisfactory explanation for the unanswered bits would not eventually have emerged.
The return of Jean Grey and the launch of X-Factor to my mind were an attempt to "fix" something that wasn't broken - I was totally okay (and excited) with the X-Men as they then were, I did not want to return to the boring dynamic that got the title cancelled in the first place. (The creators of X-Factor were so engulfed in nostalgia that they even brought the Beast's and Iceman's largely forgettable silver-age girlfriends out of retirement, tried to reinstate the Scott-Jean-Warren triangle, and returned the Beast to his original looks). And it was horribly and incompetently written to such an extent, that I think it is best compared to "One More Day", another "fix" story which set out to convince readers that Spider-Man's marriage to Mary Jane Watson was a mistake and a Bad Thing, but in the end only managed to convince an awful lot of readers that One More Day is the worst Spider-Man story ever written.
With the Pryor-Summers marriage the "cure" turned out worse than the "disease" as well. The original stories tried to destroy Madelyne (now called Maddy) as a character, but were more effective in destroying Scott. And it is not just that he was shown to be a much worse husband to "Maddy" than she was shown to be a bad wife to him, it was also that he was shown to be dishonest to Jean, the woman he claimed to love, and made Hank, Warren and Bobby his accomplices in hiding the truth from her (so much for friendship among the original five). The original five were also portrayed as judgmental and ignorant jerks vis-à-vis their teammates, the active X-Men, and total dumbasses, falling for the insane scheme proposed by Warren's villainous friend and for some reason never contacting Jean's family or Havok and Polaris.
(1) The thing was, everybody kept saying that Madelyne looked just like Jean, but to me this was not borne out by the artwork. It doesn't help that under most artists' pencils Jean is just another pretty redhead - put her in civilian clothes, and she is not easy to distinguish from Hellcat, Batgirl or quite a few other characters.
(2) Sometimes also related to Jean Grey. For instance that time after the fight against Magneto in Antarctica when Jean and Hank got separated from the rest of the team and for whatever reason both parties thought the other was dead.