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.
The death of Jean's family. It sounds like it happened in an X-Factor issue or storyline (Probably during Simonson's run.).
To answer the question, the X-universe has definitely become too convoluted in regards to characters like Psylocke, Cable, Rachel Summers, etc. I would also remove Vulcan, Wolverine's son, and Emma Frost becoming a villain again. Other things would be Longshot (He might not be a bad character, he just doesn't fit in on books. I don't think that he was meant to.), Shatterstar's origin and Nightcrawler's demonic origin, and Professor X covering up the mission via Deadly Genesis.I also liked Magneto being Quicksilver and Scarlet Witch's father, so the should have kept that. And, oh yeah, all of that confusion about Xorn (After Morrison left.).