The question is, why?
I'm not going to diss fanfiction at all. I think it's a lovely thing. I write fanfics and I read fanfics (barring porn/erotica), and thoroughly enjoy doing both. (Yes, I even read all the cheesy WAFF and Hurt-Comfort fics. Eat me now).
I think there are three main reasons for all the bad fanfiction out there, and they are as follows:
1. Lack of basic writing skills. I think that many people who write fanfiction are just starting out on their writing journeys, or else consider writing a mildly entertaining pastime, and so lack a lot of the foundation skills for storybuilding. Good grammar, plotting, character development, spelling, and a reasonable vocabulary are all needed to construct a truly good story. Fanfiction is not a good way to develop these skills; while it's entertaining and a good way to exercise your muscles, I don't think any beginning writers should make their first story a fanfic. There's just too much of an urge to not put any thought into it; to just take the canon characters, add a healthy measure of angst and WAFF, maybe throw in a Mary Sue or five, and then be done with it. The temptation isn't so great with original fiction.
2. Writing solely for others. People thrive on attention; writers thrive on reviews (at least, most writers do. I do). Even something as simple as "wow kewl story" can lift hearts. It's simply a good feeling to know that your work has been read and, hopefully, appreciated.
This can get out of hand, however. People can start writing only for the sake of getting comments, comments, and more comments. They write for attention, and writing a fanfic for a popular fandom will probably get you some of that. And, of course, the comments had better be positive, or else the poor little snubbed fanfic author will get discouraged and stop posting chapters.
3. Writing just to gratify yourself. I know this goes against the above point a bit, but it's also a problem. This, I believe, is the reason for so many Mary Sue's, perfect characters, endless flowery descriptions, pointless sex scenes, and everything else that can really ruin a fanfic. People write just to please themselves and make themselves feel good. They use self-insertions and Mary Sue's to put themselves right in the middle of the action, to surround themselves with beautiful, perfect people, to self-indulge whenever possible, and generally to satisfy ever little fantasy and dream born while while the author was wallowing in self-pity in her room, or dreaming about that one boy she's had her eye on. Writing is a discipline, an art. Although writing is certainly enjoyable, you shouldn't create plots and characters just to serve you. Let them serve the story itself. Again: write to write, and for nothing else.
If people would make an effort to avoid these things, I think the world of fandom would be a much, much more agreeable place. My advice for everyone is to handle fanfiction in the exact way you'd handle original fiction: with dedication and care. Fanfiction isn't a cheap substitute for real writing, nor is it any sort of easy shortcut. It's writing, and writing is art.
Now, if you'll excuse me, I'm going to go and write the next chapter of my Wind Waker fanfic! Thanks for the time. ^^

