I understand that an alternate reality is usually looked at as a shallow, pathetic, stupid, ridiculed, ridiculous, retarded, dumb, absolutely degrading, and fanfics that are alternate universe are ultimately looked down upon because of
automatic bias.
To be honest with you, this started as a fanfic where I got to call Tsukasa a pussy.
And speaking of Subaru, I don't think the writers of the .hack//SIGN were in exact favor of her either, actually, I don't think they were in favor of any of the characters.
EDIT: ... Maybe Mimiru, but everyone else is a bit lost at Sea.
And the fanfic isn't even finished yet, how do you know how Subaru will turn out in the end? If anything, everyone's going to get a happy ending;
including Ginkan.
... BTW - "You know, I've noticed that most AU fics are just an excuse for the author to do whatever he or she pleases with a given series or character, regardless of canon." Yes I've noticed this too. After reading too much Harry Potter fanfic. However, in an alternate reality, you're given flexibility. And you know, I'm betting you wouldn't be saying this me if I had changed everyone's name and pretended like they were other players.
Oh, and concerning the "justification of turning Subaru into a b*tch" - Tsukasa and Subaru are searching for the same thing in the actual series; they're personalities were alike, to meet that bar of Tsukasa's personality was changed to; Materialistic, Arrogant, and Self-Satisfying, Subaru's had to be changed to meet his. Although you may argue that this is because I don't like her: no, I didn't like Subaru, because the problem I had with her is that she acts as a passive, frail, person who must move around the online world of which she clings onto, while not looking for the gap to fill up her emptyness and not looking for the "color" in her real life until she is able to find Tsukasa, a perosn similar to her: in the A.R. Subaru has become frail person, arrogant and materialistic to meet Tsukasa's personality, and who moves around The World, and being less passive about it and more like, "Hey I'm disabled everyone should feel sorry for me rather than me feeling sorry for myself." They're now both searching for searching for where they belong, only... they both have different out looks on life itself. Subaru is disabled, but her disability gives her arrogance: she believes she deserves something, in specific sympathy, and most important what she's missing: "actual" power, which she has in The World. Tsukasa is abused and teased, and he wants to be better than everyone else so he can go become stronger than them and "pay them back" for all hardships he's suffered.