First off, I must start by saying I know nothing at all about Yu-Gi-Oh! and can't tell how much of this is derived from that, and how much is your original creation. This in itself, of course, is a very good thing, because it shows that this definitely works as a stand alone and does not require any previous knowledge to "get" it. That could be a plus if you were to rework this into something wholly original, I suppose.
Alright then, I'll begin by biting into a few of the characters a bit.
Starting with Joan.
She was agreeable and I liked her straight from the initial description. I don't think that you left her at all as blank a slate as you stated in the foreword that you would, though. We learned quite a lot about both her physique and her personality along the way, methinks.
The single most intriguing bit to me was that she apparently had many Michaels as lovers, and I hope you elaborate on that in the subsequent parts.
That she mostly only has sex with married men, left unexplained could give Joan a bit of a mean streak, if she is the mistress to the husband of many an unknowing wife. But I get the impression that more likely she only has sex with polyamorous married men. This, then, begs for an explanation as to why that is? Is it because she wants to keep a clean exit available for herself, so that she can leave any of her lovers? Any of her Michaels? Then it would be exactly the same as what Mokuba stated to be his reason for wanting to "date" her. But this is all left for speculation, at least for this part, but I think this shouldn't be so. I see no reason to hide such a vital piece of information which seems to not be any secret to the characters themselves.
Second character we meet is Marc. My least favorite, I must say. I felt him a little void of personality. But maybe that was intentional. At least that void actually felt like his character by the end of the story.
It was mentioned in his description that Genghis Khan was his ancestor. But the great Khan lived so long ago and has so many descendants walking the earth now that it doesn't really mean anything to be one of them. I suppose it was here to convey that his appearance was somewhat warrior-like? I would not personally use this exact description to make that point come across.
And then his wife, Laura. She was a bit more interesting than her husband. She came across as trying very hard to seem tough and to be overtly crass on purpose. Case in point, her whole conversation with Roland.
Was she actually exhibiting some neurotic behavior because of her and her husband's polyamorous relationship? Maybe she isn't as cool with the whole setup as she likes to pretend. That's definitely what I got out of it. Even Marc supports this in that one scene where he says that Laura is freaking out over that Shadow Realm incident. And this would also play well together with the void personality of Marc. Perhaps because Marc is so callous and doesn't really care about anything, it causes secret anxiety within Laura, who is obviously a more sensitive person.
I felt that the introduction of Mokuba with the brother fetish conversation paints him as something quite different, than the bashful introvert he turned out to be. Violet eyes are cool, but shouldn't Mokuba then be an albino as well? I suppose that is a Yu-Gi-Oh thing, though, and not your own?
Now, the brother, Seto. I personally disdained the guy, and for this reason, alongside Joan, he was my favorite character.
What planet is this outrageous guy from if he speaks fluent English but knows almost nothing at all about America? Except that he is probably only pretending to not know anything because he is a bit of a prick.
Seto is a major hypocrite for bring so obsessed with prostitutes but still scorns bringing one to the workplace. But then, Seto seems to be a lot of unpleasant things. Like his penchant for firing people at the drop of a hat.
And also that he prefers to pay prostitutes instead of having affairs with other women out of fear of gold diggers. This bespeaks the fact that he has a twisted sense of honor. He obviously would not be able to have casual relationships with women without paying them, or else he would have to commit himself to them. He does not pay his prostitutes for their services, really, but he pays them to leave. This is interesting. Very similar, in a way, to his brother's (and presumably Joan's) driving motivation, and seems to make it an overarching theme in the story.
This prevalence of an "exit door strategy" makes me think that the most vulnerable people in this story are Laura and Marc. Oh, yes, even callous Marc, for even he might have feelings beneath that veneer and not the sense to protect himself like all these other crafty people.
Overall, the characters had more depth than I assumed at the beginning of the story. That was good. They generally gave off the sense of a relaxed California attitude, which was pleasant. Except of course the Japanese characters who were suitably more tense.
Now for some scenes.
One I liked was the work place setting in the first chapter. I've been to a similar nerd scene myself a long time ago and this felt like a believable working environment of nerds.
The scene where Joan and Mokuba pretend to meet for the first time was my favorite of the whole story. While some of the other dialogue at times felt a little... hmm... choppy, in this scene you got it just right. It flowed well and felt pretty natural and was even quite playful and fun.
My least favorite scene was the one with the hoity-toity shop attendant. The premise of chasing away customers because he saw them as riff-raff was solid, but it was unbelievable that he then proceeded to talk as riff-raff himself.
"The fuck you do. Get out now!"
No, people like him do it way more insidiously, with much more holier than thou, nose up in the air, attitude.
One scene where I had a little trouble deciphering the characters reactions was the one where Laura was texting Marc and Joan about Seto being a psycho. It was hard to tell whether they were taking her seriously or only as a joke. I'm leaning toward the latter because of how little worry it caused for them, but their demeanor otherwise suggested the former more. To me it seemed that either they were too placid if they were serious, or too frantic if it was just a joke to them. Personally, I'd rewrite this scene to make it more clear.
Then the scene where she donned cargo pants because they were comfortable. This is very minor, I guess, and my reasoning for not liking this little bit may seem funny to you, but it's a personal pet peeve of mine. See, the problem I have with this, is that I don't think cargo pants are comfortable, and I don't think very many other people really think so either. I believe everybody just says they do because it's the general delusion and they very much like going along with what everybody else is saying. And so it irks me whenever I see a character do something like this inside their own head. It's okay if the character makes me believe that this really is what she likes, but somehow that's not what I'm picking up from Joan. From her it only feels like proliferating a myth for the sake of it being general, and I'm not buying it from her.
That said, overall this piece was pretty well written, not perfect, but never bad. Not that I'd really know anything about writing, mind. And although this was not my genre, really, the hidden depth of these characters made this a worthwhile read. Maybe I didn't read all of this quite as intended, based on what you said in the preface. A good thing, I'd say this was far more multi-layered than the preface would have me believe. Anyway, whether right or wrong, I did enjoy that which I got out of it.
I'd say you have a lot of writing potential. Definitely keep at it.