With Atlus announcing that they are going to add voice lines to all the S-Link level up scenes, I'm guessing that's why FeMC didn't get included. They said this will already have the most voice lines of any Persona game. Adding FeMC's S-Links to that would have been a lot more lines on top of that.
Whether or not expanding the voicing was a better move than not including FeMC is another question entirely.