This four year-old article on fan fiction now seems very quaint, and not just because it reminds us of a time when online culture was more or less new and magazines like Slate wound up running these types of articles because nobody cared about politics (sigh). What's quaint is that it focuses primarily on "mainstream" fanfic, the kind that more or less straightforwardly takes characters from TV or movies and creates new stories for them. "Slash" fanfic, the Kirk-and-Spock-are-lovers type of stories, are dealt with almost as a side issue, as a "subculture" of fanfic. I don't read much fanfic these days, but it seems to me that recently -- starting even before this article was written -- slash has become the mainstream; I've known people who started out writing regular fanfic and dumped it when they discovered slash. And certainly, if you conflate slash fanfic with other types of fanfic imagining romantic relationships between characters, it seems that most fanfics these days are basically "shipper" fanfics: stories written for the purpose of imagining what it would be like if two characters (or more) "got together."
Now, I have nothing against fanfic. In fact, I like fanfic, and I've read some fanfic stories and scripts that make me wish that the real shows could do something like that. The standard objection to fanfic is that it's theft of intellectual property, which seems pretty rich when you consider that TV writers get jobs by writing spec scripts for existing shows that they don't work on. When a writer writes a spec script, he's taking characters that don't belong to him and creating a new story for them -- in other words, writing fanfic. If they can do it in the hopes of getting a job and making money, why can't non-professionals do the same thing for fun?
No, my problem with fanfic is that nowadays it seems exclusively oriented toward making characters have romantic relationships with each other. The great thing about fanfic is that it allows a writer to take interesting characters and do things with them that the show, for reasons of propriety or convention or just plain ineptitude, could not do. The reason The A-Team used to have a big fanfic cult, apart from the rampant slash potential, was that it was a show where the concept was more interesting than the show: there were all kinds of dark, adult possibilities in the story of four weird Vietnam Vets working as soldiers of fortune, but the show was a kids' show where nobody ever got hurt. Writing fanfic presents the opportunity to imagine the kind of dark, gritty stories that the show could have done in an alternate TV universe.
But here's the thing: writing that kind of fanfic means staying true to the basic rules that the show has established for the characters -- to put the characters in new and more interesting situations, you have to make sure you're staying true to the characters. The best fanfics are the ones that could be an episode of the show if the show was better/darker/funnier/whatever. Making characters do things that would be totally out of character for them -- and that's what a lot of "romance" fanfics boil down to -- doesn't allow for that; instead of taking the characters out of the constraints of the original show or movie, you're rewriting the characters to be the kind of people you'd prefer them to be. And in that case, why not just create new characters and come up with stories to fit them? The justification for fanfic is that you like one element of the original show, namely the characters, but you want to change other elements. If what you come up with has nothing in common with the show, then I can't really see the point of fanfic.
The other problem I have with romantic fanfiction is that it's part of a style of TV-watching I dislike: "shipping," or obsession with romantic relationships between characters. I for one never care -- never, no never, well, hardly ever -- whether TV characters will "get together" romantically. I didn't care about the romantic prospects of Niles and Daphne or Buffy and Angel (the wussiest vampire ever up to that point) or Buffy and Spike (holder of wussiest-vampire-ever honors from 2000 onwards) or, for that matter, Kirk and Spock. Buffy is a good case in point because the romance elements were almost always the worst part of the show (the "evil ex-boyfriend" scenario from season 2 was the only good romantic storyline), and yet to hear many fans and even some of the show's writers talk about it, all we were supposed to care about was who was getting together with whom. As the show went on, boring romances overwhelmed the good stuff, until the characters who mattered -- Buffy and her friends -- had more scenes with their romantic partners du semaine than with each other. That's the way I feel about fanfic: with so many potentially interesting storylines you could create for the characters, free from all the bounds of TV and movie convention, budgets, etc., why do 95% of fanfics go for the same old I've-always-loved-you routine?