There are great stories people write that have honestly better thought out stories than some triple A games, but then there is the weird ass shit that just buries those gold bars.
Id argue everything is like that, somethings are great others are downright awful. but out of curiosity what fanfic have you read that you consider great?
I write my own fan fics, and I just stay away from romance. That's what tears a lot of fans apart, and I don't like witnessing that. Although, I even confuse myself writing sometimes because there are so many elements that have to stay canon. Fan fics are just confusing, let's just go with that.