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."
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.