Man, so many dumb ideas. Maybe I'll break it down by book:
Captain America: Cap armor and new shield.
Iron Man: Tony Stark dies, only to be replaced by younger Tony Stark.
X-Men: Xorn/Magneto debacle....although, I think the different direction the books took after X-Men the Movie came out pretty much was a bad idea. I think that's when we first saw Xorn, and the Xavier school just became overrun with tons of mutant kids. X-Men has never reclaimed the glory it had for me since then...even Astonishing X-Men is only so-so.
Fantastic Four: The worst thing I've ever seen was the female Thing. It still gives me the creeps.
Hulk: I really didn't like the whole idea of "Bruce Banner is dying, and you don't know which version of Hulk is going to emerge." The stories weren't bad; but, it always seems like a bad move to have your main character supposedly going to die in the near future. We've seen it done with Captain America, Iron Man, and many others. They never die...or, if they do, they come back, ala Superman, soon enough.
Spider-Man: I was going to say The Other...but, Sins Past was just soooo bad. Both of those make The Clone Saga seem so much better, I must say. Bring back Scarlet Spider!!!!
Avengers: Bendis and the New Avengers....nuff said.
Daredevil: "Fall From Grace" storyline and everything after, until Kevin Smith came along to start up Vol. 2. I remember when the storyline and new costume came out, it was really in high demand...but, the stories were just crap, and it really is a big blemish in an otherwise great, great comic book.
Defenders: The New Defenders. When the book changed direction and it was told that the original members of the Defenders could never team up again, or disaster would strike, the book became very unreadable. There is a reason the final issues of Defenders Vol. 1 can be still found in the quarter bin.
Ditto.
