*slides briefly out of lurking* A few days late to be replying to this, but couldn't resist slipping in a rec. The best YGO gen author I've found, hands down, has to be Vathara (http://www.fanfiction.net/u/77482).
She doesn't write straight YGO, however -- crossovers are her method of choice (unfortunately, perhaps? dunno how you feel about x-overs). Very well-written crossovers, though, and the crosses make sense when read -- in order (it's all one big universe): Foreign xChange (cross w/X-Men), Whistling Past the Graveyard (companion to Fx), and Roll the Bones (sequel, cross w/Sentinel), w/ a couple scattered side stories. ^_^ (also -- don't know how far you've gotten for YGO? just a warning, the fics can be pretty spoilery)
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She doesn't write straight YGO, however -- crossovers are her method of choice (unfortunately, perhaps? dunno how you feel about x-overs). Very well-written crossovers, though, and the crosses make sense when read -- in order (it's all one big universe): Foreign xChange (cross w/X-Men), Whistling Past the Graveyard (companion to Fx), and Roll the Bones (sequel, cross w/Sentinel), w/ a couple scattered side stories. ^_^ (also -- don't know how far you've gotten for YGO? just a warning, the fics can be pretty spoilery)