I SO agree with Iceechan on shipping fics. Why do people even call them pokémon fanfics, usually they don't involve pokémon in them at all. I don't really think all those kids on the pokémon show are something to make up love between and write fanfics about it, anyway.
Fics that stay too closely to the plot of a game or the show, it's way too inoriginal and I think it pretty much tells you that the author has no decent imagination, unless it's a parody (then it can be really funny).
I hate it when everyone always gets a starter from a professor. If you HAVE to have a professor, you can at least make the main character get a special pokémon for some reason, that will at least make half of the beginning original (but no waking up late and getting a Pikachu, please).
But what I hate the most is when pokémon are put into fics there like little robots that have no purpose except making the fic into a pokémon one and getting an excuse for the main character to travel. Pokémon are characters and need a personality, and then I mean a real, deep personality, not just being obsessed with ice cream.
Legendary pokémon should not obey a little kid if they don't want to and aren't forced to. If you were a legend and some kid stuffed you into a ball, you wouldn't just go by everything they say.
Well, really, I have to put fics based on the games in here again, this time for a different reason: the pokémon games aren't about plot. They don't have a decent plot the game revolves around, just a team with an evil plan. Meaning that if you're going to base a fic entirely on a pokémon game, the fic won't have a decent plot.
Constantly confusing things like "their" and "they're". "Their" means that they own something so it's theirs, and "they're" is a shortened version of "they are". I hate reading something like that, it's irritating to have to stop by every "they're" and "their" figuring out what it means this time.