New X-Men/YMMV

Complete Monster: For Xorn/Magneto, herding New York's human population into gas chambers was just a warmup for converting the entire Earth into a mutant haven (and annihilating humanity as a result).
- Cassandra Nova. The woman has been out to murder Charles Xavier ever since they were in the womb, and orchestrated the death of the entire population of Genosha. She also employs Mind Rape on both Beast and Beak, taunting Hank that he's devolving and will become less and less human, while she forces Beak to beat Hank near to death with his bat, all the while Beak is tearfully aware of what he's doing and begs Cassandra to make him to stop.
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.
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.
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?
Love It or Hate It: Depending on who you ask, the series is either a bold, much-needed fresh take on the X Men mythos that brought it out of a decade-long Dork Age and finally brought it some Character Development and new ideas...or a convoluted, barely comprehensible mess that's X-Men In Name Only.
Retcon: Xorn's reveal as Magneto was hastily swept under the rug as soon as Morrison's run ended. This was parodied in the fan film Death Becomes Them:

Magneto: No, that was actually Xorn's twin brother, possessed by the sentient mold Sublime, pretending to be me, pretending to be Xorn."
Beast: That defies all logic!

They Wasted a Perfectly Good Plot: "Here Comes Tomorrow" could have been used for some cool speculation about the X-Men's future and the impact that their struggles might have on the world, but it's instead used for a completely nonsensical slugfest between a bunch of newly introduced characters who get a pointless Kill'Em All ending, it raises more questions than it answers (Ernst is revealed to be Cassandra Nova and the Stepford Cuckoos are revealed to be Weapon XIV, both in throwaway lines that are never elaborated on), and its only real impact on the series is that it kicks off Scott and Emma's new relationship by "revealing" that the universe is doomed if they don't hook up. For some reason.
Too Soon: A few fans saw Scott's burgeoning relationship with Emma as this. Particularly since it featured her kissing Scott over Jean's grave a day after she died...making snarky comments like "How many times have you buried her now?" and "This must be getting rather tedious for you," all the while.
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.