These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: New X-Men
Author's Saving Throw: "Planet X" was subject to a well-known (for being ridiculously confusing) one of these almost as soon as Morrison left Marvel. Morrison himself may have acknowledged that one of these would be necessary eventually, as within the story itself the only character who seems absolutely sure that "Magneto" is who he claims to be is Toad.
Creator's Pet: A common criticism of "Here Comes Tomorrow" is that it's billed as the ultimate Grand Finale for the X-mythos as a whole, but the only previously established X-Men characters appearing in it (outside of the five core members of the present-day team) are characters created by Grant Morrison himself in this very run. Naturally, an X-fan reading it might hope to see what happened with some of the X-Men's descendants in the 150 years since the team disbanded, but the only one we get to meet is Tito Bohusk, the grandson of Angel Salvadore and Beak.
Morrison often seemed to favor his own characters over the established ones, particularly the Cuckoos, who get to save the day as often as some of the preexisting X-Men. It's subverted in the sense that many other writers have since used these characters and entrenched them as permanent additions to the greater mythos, and most of them have strong fanbases besides.
Die for Our Ship: Jean Grey is abruptly killed off by a single touch on the shoulder from Xorn/Magneto (just one issue after she survived being hurled into the sun, no less) to make room for the new Scott/Emma pairing. It's justified in-universe by the revelation that Scott and Emma not hooking up will lead to The End of the World as We Know It, and a ridiculously convoluted plot in which Jean's spirit psychically forces Scott accept the new relationship without complaint. Apparently, gradually easing them into the relationship wasn't an option—Jean had to die right then, and Emma had to make out with Scott the day after it happened. On top of Jean's grave.
It should be noted that Morrison did not do this because he himself disliked Jean or preferred Scott with Emma (in fact, he expressed in interviews that he had several more stories planned for Jean had he stayed longer). Rather, it was because those higher on the totem pole than him felt Jean was too powerful and thus had to be removed.
Fanon Discontinuity: Invoked. Morrison has gone on record as saying he deliberately wrote "Here Comes Tomorrow" in such a way that readers could consider it the very last X-Men story if so inclined.
Hollywood Pudgy: Angel Salvadore. Both Ethan Van Sciver and Frank Quitely drew her noticeably chunky around the middle without being overweight. Wolverine once quipped that he would've kicked her butt if it didn't wobble around so much.
Holy Shit Quotient: The entire series was built on this - it started with Genosha (and its population of several million mutants) being wiped off the face of the Earth by Sentinels, and climaxed with Xorn revealing himself to be Magneto and attempting to go kill every human in New York as the team rushed to get back together and stop him.
Jerk Sue: A common complaint about Emma Frost's characterization in this series. She takes advantage of someone's mental health to seduce him into a telepathic affair that destroys his marriage (as well as his relationships with his biological daughter and some of his friends) and starts openly dating him immediately after his wife is violently murdered. Her actions immediately get excused because "she loves him", and she ends up in charge of the Xavier Institute by the end.
Like You Would Really Do It: Wolverine's fate at the end of the "Assault On Weapon Plus" arc. Because there's going to be doubt whether or not he survived the explosion?
Parody Sue: Fantomex, who is essentially a ridiculous amalgamation of pretty much every trope commonly found in Marty Stus. Morrison also deconstructs the Marty Stu to an extent, with the revelation that Fantomex was built like this by Weapon Plus, who knew that it would be easier for the public to stomach the mass killing of mutants if it was done by a cool, likable superhero.
Recycled Script: Eagle-eyed fans have noted that Sublime is quite similar to an old Avengers villain called "That Which Endures," another ancient, microscopic sentient lifeform that claimed to exist in all living things and to have guided evolution and attempted to control mutants. However, they have rather different modi operandi (That Which Endures wanted to make the jump from humans to mutants, whereas Sublime wanted to destroy mutants because it could not make that jump) and separate entires in the Official Handbook of the Marvel Universe, throwing the idea that Morrison intended them to be the same character (if he was even aware of That Which Endures at all; the story was very obscure and didn't have anything to do with the X-Men) into doubt. A somewhat similar character also appeared in the final issue of X-Man.
Screwed By TheEditors: When Morrison first got the book, he stated that he wanted to have a run at least as long as Claremont's first: seventeen straight years. He lasted three, due to getting into a fight with the editors over the creative direction of his character Marvel Boy. The differences proved irreconcilable, and before long Morrison did the unthinkable: he signed an exclusive with DC. Naturally, he hasn't been seen at Marvel since, and what's more, many of the changes to the X-mythos he made were quickly retconned or swept under the rug, a move Morrison himself reportedly believes was done to spite him for leaving.
A "psychic parasite" that's also Professor Xavier's stillborn (but not really) Evil Twin sister, who grew up as a blob on a sewer wall and looks like a five foot tall clone of the Professor with breasts.
A 4 billion year-old sentient supercolony of bacteria masquerading as a self-help guru, who talks to a floating brain in a jar.
An elderly Chinese military officer who creates clones of himself with his dandruff flakes and gets his kicks watching naked women wrestle each other covered in crude oil.
A masked French thief whose best friend/lover is a talking Flying Saucer who crawled out of his mouth when he was a child.
A talking Scottish whale with psychic powers. Who's also a superhero, apparently.
Win Back The Crowd: One of the main goals of the series, as Morrison states in his outline for the run. After spending years as Marvel's most popular book (and one of the most lucrative superhero franchises on Earth), X-Men hit a bit of a Dork Age in the late 90s as editors began enforcing Status Quo Is God a little too much and falling back on old cliches to avoid losing a successful formula. With New X-Men, Morrison sought to take advantage of the new interest sparked by the movie to bring the series to a wider audience while resurrecting the wild, experimental storytelling that made it popular in the first place. Though the run is polarizing amongst long-time fans, it revived dwindling interest in the X-mythos and saw a huge boost in sales.
The Woobie: Almost nothing goes right for Beak - he was traumatized as a kid when his powers manifested, got teased by kids, was forced to beat Beast nearly to death against his will, decided to follow Xorn because he looked up to him, got the crap beaten out of him when he left, and finally got beaten again by Magneto during the assault in the "Planet X" arc. About the only good thing that comes out of this is a relationship with Angel.