One of my problems is the now now now rush of the potentially good storylines. Orton went from Evo member to world champion to not-Evo member in the course of 24 hours, and then to not-world champion in a month. Conceivably the storyline could have gone on for a good while longer than that, but the WWE felt the need to rush rush rush it and it lost a lot of potential impact.
Or when a thrown-together tag team breaks up only a month after being created and they expect fans to care about the breakup and whichever members turn heel/face... the Rockers break-up, it's not.
Ironically, of course, it seems the worst storylines (Test-Steiner, Torrie-Dawn) are the ones allowed to go on forever
Another one is when horrible inconsistencies come up in storylines... I'm not talking nitpicky type things, but egregious things like when all the Divas inexplicably dropped their feuds/hatred of each other to unite against the Diva contestants