Boycott Atlus

[Solid Snake]

Heck, there are ways for an author to inform the reader that 'homophobia / transphobia is a character flaw' even in the context of writing a homophobic or transphobic character who never receives a literal or metaphorical karmic comeuppance. It's much tougher to write, and it requires a degree of skill in narration that I doubt most writers possess (let alone the ones employed by Atlus), but it's certainly been done.

You can have Yu get all the ladies, all the respect and all the friendship is magic and still have an undercurrent in the narration of "It's totally not okay for Yu to be homophobic, and the fact that society still adores him unequivocally despite his prejudices is society's fault because society is shallow and superficial and prejudiced." Writers have a lot of tools in their arsenal to attempt just that feat, but the degree of subtlety makes it a better approach in literature than in a mainstream, mass-market video game.