I've read somewhere around 15,000 fanfictions in about twenty different fandoms and thus hold stories to extremely high standards. So far (with a few exceptions such as "Pretty in Pink") every thing I have read in this fandom has been mediocre to average. If your story has some how ended up on my favorite list, consider it an accomplishment. Less than .01% of fanfictions make it on that list.
My biggest problem with fanfiction in general is plausibility. Be it how in-character said character is to weather or not the author has taken his or her time to DO THE RESEARCH needed to pull off a good fic. In my mind there is NO EXCUSE for this.
And what is it with shipping in this fandom? I swear, it's worse than what goes on in the "Naruto" fandom!