I personally feel as though Shuu would have ended choosing to be a girl. While yes she would have thought about picking male for a while the fact arises that she has lived her entire life as a girl, she wouldn't know anything about the standard way a man lives. Not to mention the fact that she met Youko as a girl, for her two girls being in a relationship may seem more natural, you can see that she was very worried about becoming a man, so if someone told her that two girls could be in a relationship then I think she would decide to stay female.
In my own head I decided that after these events Shuu, Youko, Misori and the girl that confessed to Youko ended up with a lovable foursome relationship, while Aika and her friend got together as well.