Inspired by chicanery asking the high points, let's lament the lows:
The Clone Saga with the exception of Ben Reilly, Kaine Parker and JMD's stories.
Sins Past and One More Day. The two worst Spider-Man stories ever. Painful to say as I have JMS as one of the best Spider-Man writers ever. I know JMS is very divisive.
Alpha.
Brand New Day.
The cancellation of The Spectacular Spider-Man (2008-2009).
Silk. I hate that character.
TASM (Vol. 3), TASM (Vol. 4). Absolutely awful.
The treatment of Ben Reilly under Slott, PAD, Lowe and Wells. I'd rather he had stayed dead with the exception of JMD's miniseries.
The editorial interference in TASM (Vol. 5).
TASM (Vol. 6).