Actually, one reason for designing the new combat system in the way that I did (more focus on the girls' personalities, tying them directly to locations) was so that I could incorporate them into the events that occur in those locations.
People embraced the Boss Girls way more than I thought, so screw it, I'm embracing that ;)
Don't expect the Boss Girls to rise to the dizzying heights of Main Girl status, but do expect to see them a lot more in events that occur in those locations, including events that involve actual Main Girls :)