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Although by tvtropes definition, it technically isn't fanon (but still scary nonetheless). Ultimately, those types of sites like the Pikmin fanon one really just boils down to fan-fiction. Some good, most bad, although your mileage may vary. I usually go on that Pikmin Fanon site if I'm incredibly bored; the shock at some people's ideas usually wakes me up.
EDIT: Oh yes, I totally forget, check this page out:
Arguably, there are SOME good ideas in the Pikmin fanon, but it's just chock full of wierdness that wouldn't really fit in a game. Example: an Onion seed, which you have to spend days and days watching just so you can get an Onion to store Pikmin you get from the Candypop Buds.
Are you kidding me? What could possibly go wrong?!