In addition to a bunch of stuff already mentioned, there is another character issue along the lines of "Mary Sue" (don't know if it also has a name) that I find really offputting. It's when the protagonist, or sometimes every major character, is just so, so, so quirky and unique. As in "lives in a treehouse and relies on a unicycle for transportation and wears deliberately mismatched vintage clothes and makes a living writing poetry that he/she sells it at subway entrances while singing obscure opera selections and was raised in a commune in Alaska and..." Okay, I'm exaggerating, but it does get tiring. Interesting characters are one of the great things about fiction, but I can only suspend a certain amount of disbelief.
And this isn't so much a pet peeve as a generalized dislike: magic realism and similar story-telling mechanisms that aren't disclosed upfront. A couple of months ago I picked up a book that looked interesting: set in late 19th or early 20th century, family living on semi-isolated estate has to shelter some victims of a train wreck, someone from the mother's past turns up with a secret that could blow the family apart...it sounded promising. Then it started to devolve into the supernatural, which had not been hinted at in any of the plot descriptions, and I felt quite cheated. If I wanted to read a ghost(ish) story, I'd have picked one.