Fun reading through the thread! My take:
X-Men: A- at the time, B in the context of the whole series. The Xavier/Magneto rivalry and the Wolverine intro were great. Comparison of the Holocaust to Mutant Registration was a great idea.
X2: A, except the Oval Office scene would have had the president immediately ordering Sentinels.
The Last Stand: F. From Cyclops' early and unmourned death to the very non-cosmic, flunkie version of Phoenix, this film seemed determined to botch one of the three or four most famous storylines in comics.
XO: Wolverine: C+. It was fun to watch Jackman anyway.
First Class: B. McAvoy and Fassbender were great. Quicksilver was fun. Mystique was shoehorned. Bacon was embarrassing.
The Wolverine: B+. They didn't totally blow the only Wolverine story I care about. I can tolerate the robo-Samurai as an homage to anime fascination with that trope, silly as it is in live action.
Days of Future Past: A+. The future fight scenes showcase everybody in a setting where lack of character development doesn't matter much. Dinklage is great. Mopey Xavier got nice moments. Mystique was still shoehorned.
Deadpool: B+. Some of it was really clever. But these improvisational comedies (shoot the scene 50 times and splice together the best jokes) always end up mistaking vulgarity for humor. Great Colossus. CGI was a wise choice.
Apocalypse: F. So bad. The villain is a boring mustache twirler who wants to destroy the world, and half the characters join that scheme for no reason, Quicksilver's shtick is just has lost most of its humor value when repeated note for note. I did like Nightcrawler and Caliban.
Logan: A-. The four heroes played it so well, and I especially loved Caliban. But the villain was meh, and the tone was so unremittingly grim that as soon as they went home with the nice farming family, the by-the-numbers tragedy ahead was cliche. Bonus for near-future self-driving transport trucks.
Almost all of the continuity problems come down to one basic problem: Lack of vision. There's no grand architect, no confidence that there will definitely be a next film, so you can set things up now with confidence that you can knock them down next time. That's how you end up with three different actresses playing Kitty Pryde, who (IMHO) ought to be one of the central characters of the series, at least in one of the time frames. That's also how you get Magneto and Mystique shoehorned into stories like Dark Phoenix where they're worse than unnecessary, but actually end up thwarting the central plot of each film. (The is worst in The Last Stand and Apocalpyse.)
I would love to live in a universe where Fox did for X-Men what Disney is doing for the MCU. More films closer together (annually?) with no expectation that you have to have Magneto or Wolverine in every one of them just because Fassbender or Jackman has demonstrable star power. More movies means you see enough of your favorites but then get stories that don't make sense with them too. We don't need Captain America in Guardians of the Galaxy. We don't need Thor in Captain America 3.
This is particularly important for the Dark Phoenix story, which is not about Jean's powers changing, but rather is about Jean's character changing. Joss Whedon understood this, and he pulled it off perfectly over the course of Buffy. You have to show the good girl being good for a while. You have to make us love her as a good girl. Then we care when she goes bad. It's a genuine tragedy that resonates deeply; we've all seen loved ones go off the rails.
Ratner gets blamed for botching Dark Phoenix, and to some extent that's true. But I also can't fault him for not paying off what was never set up to begin with by Singer. There's only so much you can do in one film. The first film established the basic "persecuted minority" conflict and made lots of room for fan favorite Wolverine. The second film basically did the same thing again, except with humans as the instigators rather than mutants. But they devoted so little attention to Jean and Scott that there was nothing characterwise to grab onto for the third film, which I'm sure is why Scott was pointlessly killed early on; Singer had failed to give him a reason to be in the film, and that was a bad sign before Ratner was ever hired, in retrospect.
We didn't see Famke ("Dr. Jean Grey, academician, mutant expert before Congress") be good; she was just kinda boring, and attracted to Wolverine from the get-go. We never see her and Scott happy together, throwing popcorn at each other while they watch a movie or something. Then maybe Wolverine shows up and she starts to feel conflicted. For whatever reason, her powers grow over the course of a couple of films. Maybe makes a couple of Dark Side type choices, earning concerned looks from Scott and Charles and even Logan. Then some villain hurts her parents, and she goes nuts, kills the villain, fights the X-Men, flies off to eat the D'Bari system, attracts Shi'ar attention, and bam, some version of Issue 137 unfolds.
Singer just doesn't resonate with the "corruption of innocence" Phoenix story, as is obvious from Apocalypse, which still doesn't set Jean up characterwise; it just shows her power ramping up. So again next time we're going to show her go berserk, but we probably still won't care, because we never really knew her before.
Warner Brothers has been hit and miss with this, trying inconsistently to follow Marvel's lead. I finally saw Suicide Squad last week, and one of the worst things about it was the lengthy-yet-rushed introductions for each character. If the DCU knew what they were doing, then Joker and Harley Q would be in a Batman movie first. Likewise the other villains. They get defeated in separate stories, then their own movie brings them together, like a true anti-JLA. (Next time, some up with a believable reason you'd choose Harley Quinn to be on the team fighting the demon wizards. Maybe some special thing she knows besides how giggle.)