For me in no particular order:
1. Cable and everyone from his timeline.
2. The Phoenix Force...I just loathe any story where it's a crucial plot point.
3. The O5 X-Men
4. Cassandra Nova...she was just a bad idea.
5. Left over Age of Apocalypse characters. It was a great story. I don't want to ever see any of them again.
6. X-23 (the concept just seems silly to me...always has)
7. The deaths of the original Generation X members. I always thought Skin's death was particularly unfair and depressing. He was just thrown out like trash.
8. Madelyne Pryor's descent into evil. I really didn't like that. She was made evil to justify Scott being a crappy husband who bails on his family. I liked Madelyne fine when she wasn't evil.
9. The slaughter of the Grey family at their family reunion. That was really f*cking depressing and I don't think I've ever been more disgusted with a story. The story even has Jean Grey's mother dying hating her daughter. Hate hate hate it.
10. Hope Summers
Honorable mention to other things I hate: Old Man Logan, that whole Revanche storyline, kid Apocalypse, anything third Summers brother related and Moira's death.
I would like to switch the writers of The Teen Titans with the writers of the X-Men.
Therefore, Bob Haney would shepherd the X-Men and Roy Thomas would be the main writer for the X-Men in the 70s. In the 1980s, Marv Wolfman and George Perez would be the writer/artist for X-Men and Chris Claremont and John Byrne would be the New Teen Titans writer/artist. In the 2000s, you'd have the New Teen Titans Animated Series on Fox and the X-Men Go on Cartoon Network.
This would be really odd and fun.