What ones do you have? Me:
~Obvious character bashing.
~OOCness. And yes, you can be OOC without character bashing. It especially annoys me when someone tries to take Lance and turn him all dark and cruel - it is possible to develop a character more than he is in canon without completely contradicting everything we know about him and his personality. (example: we know he's good with battles, has a low tolerance for cruetly to pokemon, and seems to like people; so don't make him a sexual poke-predator who shakes babies on a regular basis. Does he get along with his mother, who maybe wants him to settle down and get married? How is he with flaky teenaged girls and bratty little kids who aren't his fans? Is he ever reckless; would it be unrealistic to do something irrational for fun during periods of dull peace?)
~Villains being portrayed as flawless saints. *twitch* They do bad things in canon. Portray them as victims, give them a few redeeming qualities to remind us that they're human, okay, but if you strip them of all cruelty, questionable morals and responsibility for their actions, then why did you decide to write about a villain in the first place?
~CrackShippings with unrealistic premises. I don't mind CrackShipping by itself, but it has to be very well written for me to like it.
~Original Trainer journeys. I generally read fanfiction to read about my favorite characters, not ones I've never heard of before...
~AU stories that have nothing to do with Pokemon, the Pokemon world and are inconsistant with Pokemon characters' pasts, but are cast with Pokemon characters. What's the point? You might as well write straight fiction. I mean, AUs are fine to a point, but when it gets to the point that you might as well invent your own characters who could fill the same roles just as well, then it starts to get on my nerves.
~Crossovers. Have yet to run accross a good one.
~Bad formatting/ grammer/ spelling, etc.. I think you should have this stuff down pretty well before you start writing fanfiction >_<. If English isn't your first language, then get a beta.
~The notion that dark = good. It doesn't.