I may put fic in comments later, but here's what I've got.
I just wrote a fic called "Leading, Leading", which is about a female Wataru trying to get Mio to be a little more courageous. Here's what I know about the universe:
* Maya left Wataru a lot earlier than she did in canon, and much earlier than I like to have her leaving Wataru. Wataru has no memories of her biological mother.
* Instead of leaving her on her own with Kivat to raise her, Maya decided to go somewhat the same route with Wataru as she did with Taiga. Wataru got adopted by Yuri (who never had Mitsuhide, but did have Megumi).
* Incidentally, Yuri's family keeps running into these strange things because they're related to the Aso family of Fatal Frame, I think.
* Wataru met Mio at a young age, probably five or six. They were in the same violin class. (Learning by the Suzuki method, of course.) They realized that they were in love in their teens. Yuri doesn't know what to make of Wataru's sexuality, but Shima is privately pleased that she's not having kids.
* Mio's parents have met Wataru and they think she's Fangire. They also really like her. Mio has an older sister named Mayu, so there's no pressure from her parents to marry a boy.
* Taiga never met Wataru in this timeline. He knows she exists because of a chance photo of Maya and a two year old Wataru. He'd like to find her because she is his baby sister. He's been watching Wataru and Mio because he can't make up his mind as to what Wataru is, and he feels responsible for the fact that there's no Queen. He doesn't know that the girl he's unsure about is his sister.
* Bishop is discouraging Taiga from chasing her down.
* Wataru knows the basics of fighting, but doesn't want to join Aozora.