I don't get the sense Akari was ever an actual boy in the first place, since she talks about it like its the reality she's been hiding for so long, and no explanation or recollection is given to when or why she changed genders.
She was just a tomboy who loved a hobby commonly seen as a male activity. But she lives in what's meant to be an in-universe equivalent of Japan where expectations of what boys and girls must be like are more strict, as she was force to wear a skirt when starting middle school and her mother insisted she now act and talk like a Yamato Nadeshiko. The story is about her realising that being a great Pokemon Trainer doesn't mean you have to look cool, or tie that to masculinity, and you also need a kind heart, which isn't a bad trait or be tied to femininity.
Long story short: Pikachu is a cute, strong, amazing and loyal Pokemon that you are lucky to have!