Yeah... I think one of the reasons why this is bugging me so much is that the Twilight fanfics being pulled from the internet are the ones that are most popular (I think 'Master of the Universe' aka '50 Shades of Grey' got something like 15,000 reviews online)... however, they are not necessarily the fics that are good enough to be published.
They're popular because they contain lots of sex and very little plot - which is fine for fanfic, but not for mainstream publishing (there's one scene I've heard about in this particular fic/book which makes my stomach turn to think about... it's something totally inappropriate for mainstream publishing, yet it's still in the book!). If it were me, I would be mortified at the very idea of my name being associated with it in real life and I think it's embarrassing for the fandom in general (especially as it's becoming publicised that it used to be a fanfic)

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On the other hand, the Roswell fanfics in this fandom that are the most popular and that people generally consider good enough for publishing are those that actually are good - they are well-written and have great storylines; they don't just focus on sex and nothing else.
The other main reason that I have a problem with it (which I've probably already mentioned in this thread) is that there is a reason we put disclaimers on our stories... because fanfic is a derivative work; we don't own the characters and part of the reason it's generally accepted by the original creators is because it's just a hobby, a chance to express your love and enjoyment for a particular book, show or movie... it's a not-for-profit endeavour.
If you want to hone your writing skills through fanfic, then that's great... but if you want to publish a mainstream novel, at least write something original - don't just publish a fanfic which could be linked back to fandom and possibly considered to be a derivative work with different names, but take what you've learned from writing fanfic and use it to create your own characters and plots instead (or take the basis of a fanfic you've written and then re-write it and create something original out of it).