Tear Jerker: Aya's backstory She's kind, bright, diligent and studious, just what you'd expect in a class representative, but she's also a Stepford Smiler steeped in self loathing because her whole family (herself included) consider her nothing more than a Replacement Goldfish for her deceased older sister. She doesn't allow herself any credit for her own actions and firmly believes "The real me is ugly."
Sagara's character arc and reasons to ultimately identify as female can be very alienating to Western readers, not only because of different views of genderqueerness, but more general philosophy of individualism versus harmony. Basically every reason given for Sagara to follow the Second Law of Gender-Bending is based on how they fit into the environment around them (what Kurokawas finds attractive; what will make dating Narumi more socially acceptable; positive changes to Sagara's lives where their sex was incidental), not their own self-perception. Sagara's ultimate decisions—that they're a girl even if they wish they were "still" a boy—is fundamentally nonsensical to most definitions of gender identity.
