To me its awful grammar, OCC characters, some fanfictions crossovers, gratuitous character bashing, emotional Mary sues that cries a lot, songfiction, fan girl ocs with superpowers, oc characters with ridicules tragic past, ANYTHING doing related to Opitmus Prime's long lost daughter, and unjustified crack..
I especially hate overly emotional human mary sue female ocs that are overpower, stupid, have emotional problem (like crying and spazzing alot), have a traumatic past, and always butting into everyone lives. Many of them claiming the secret lost daughter of a cannon character! Any character like that destroys a good fan fiction.
Sure, grammars bad when you can't even read it, and gender bending is awkward (but fun) when it's not all of the characters, the worst is OOCs. It makes me wonder whether they even know what they're writing about.
ALL of these things. I really can't stand bad grammar and when they constantly make characters OOC. I can almost live with Mary/Gary Sues. There's no excuse for bad grammar. A few mistakes are one thing. But when everything is a huge run-on sentence and there's no capitals or periods or commas anywhere, I can't even TRY to read it. And OOC...well, sometimes it happens by accident. But complete turnarounds, I can't handle. I don't even like Shattered Glass. In my opinion, if you're going to manipulate a character that much, you should give it a different name and color scheme and make it an OC. To me, the golden rule of fanfiction is that you're using someone else's characters, so you'd better keep them in character.
Also, Mpreg just confuses me. Especially Transformers. Oh, and I hate it when people write Transformers smut and they all have human parts. I mean, it just doesn't make SENSE. :icontearmyhairoutplz:
Sometimes genderbending can be amusing, if it's done right.
And none of that "I'll make them vampires/cowboys/Beanie Babies/Norse gods" stuff. Sometimes the art can be interesting, but for the most part the fanfictions end up badly written and don't make sense.
I hate all of them. Except for the Naruto one. :I Some of them are really good, especially with all the childhoods and depressing stuff in their backgrounds. Vampire...meh. I only hated them because of twilight. Buuuuuut. Some stories like The Chronicles of Vladimir Tod make it nice again(: and Adventure Time!