You do realize you're talking about one of the most revered storylines in COMIC BOOK HISTORY, right?
He created the Phoenix and killed Jean... the first time. Most of what happened after that was out of his control.
And no, no one hates on Storm for some sexist reason. Most folks that hate on Storm do it because she was hammered down their throats by types like Claremont. Just like people currently hate on Wolverine because he's essentially been portrayed as indestructible and unstoppable.
1. The fact that the Phoenix storyline is revered does not change the fact that Jean Grey is the number one beneficiary when it comes to Claremont's "exaggerations". She still went from being a side chick to God like in power. Also, remember it wasn't Claremont's idea to kill Jean Grey. That was the editor's. It is quite possible that these powerful feats would have continued in the future. The whole storyline about Storm losing her powers is what Claremont wanted to do with Jean initially. If Jean wouldn't have died maybe she would have been "shoved down our throats" but that happened anyway.
2. Many of the XMen have been portrayed without flaws or as all powerful at some point. Initially it was Professor X saving the day with his mental powers, then Cyclops with his powerful beams, Alex and the whole Monolith thing, Jean with Phoenix powers, Wolverine with his healing (and didn't he possess cosmic powers at one point), Iceman somehow being an Omega mutant, Nightcrawler being able to seemingly escape every thing thrown his way. Rachel taking out Galactus and the Beyonder, Psylocke coming back from the dead and all the other invulnerabilities she has now, Dazzler seems to be stronger than I remember now too, Sage going up against the Fury in hand to hand combat, anyone with the last name Summers being the most powerful mutant ever. Again, Storm has not been the only one and her exaggerations have not been nearly as bad or even shoved down our throats as much as others IMO. (You made this point by stating that all of the Phoenix manipulations were post-Claremont, the same people that downplayed Storm's powers, that's also close to 20 years of history.)
IIt's a comic book and overtime abilites get stretched I mean look at Superman, what once was super isn't anymore and he was boosted big time from his beginning days.
Ultimately, what works for a story is what the writer does and sometimes they downscale characters and sometimes they upgrade, its just a matter of what they need.
BTW, I am done with this discussion...this book has been really good and I would rather turn my attention to it.