That's true. Azusa Kido, the game director of Persona 3 Portable and writer of FeMC's route, I think would be a really good choice to handle Persona 6. Kazuhisa Wada is currently in charge of the Persona series, whose main body of work is the spin-offs, but Kido seems like who I would trust. She told Soejima to not focus so much on making the FeMC "cute."
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The transphobic scene at the beach in P3 is completely cut out of the FeMC's route as well. Whether or not that was deliberate, it's a good sign at least.