I don't know anything about that Sailor Moon S game so I can't comment on how similar that would be to my idea.
My line of thought was like FF 4 or 6. Your party is a subset of all of the various characters. Throughout the game party members come and go based on the plot, and at some point closer to the end of the game you have your free choice to build the party you choose. The large list of characters from PMMM and its spinoffs would be great for this since that gives you a wide variety of character types or "classes" to pick from.
I prefer RPGs in which the characters themselves are distinct from each other, and you customize your *party* rather than customizing the role/job of each specific character. I think RPGs where each individual character is a blank slate and can be configured however the player likes to be not as interesting. It kind of ruins the appeal, IMO, when the mage-looking characters do as much physical damage as the big burly ones. (e.g. FF 7 or 12). It reinforces the character designs when their game stats match their look & behavior from the anime. And the PMMM universe has enough characters that players would be able to pick whatever kind of party they might want.
In a similar style to FF4 or 6 each character can have a unique special skill too. For example, Sayaka could have some kind of healing or regeneration special ability. Kyoko might get a some kind of buff ability or special attack, Homura gets the ability to use guns or explosives, etc.>>14399