Savin has mentioned that Cait has a big expansion coming up which will include the option to change her setup to 'Red Mage' if you don't need her as a healer and Kiyoko just got a mix of alternate skillsets you can choose from. I don't think it's been said explicitly whether there are plans to do the same for Ryn but I'd be pretty surprised it it didn't happen either during the Winter City quest or as a potential reward for completing it.
I've had to resist the urge to do that with my Black Mage champion file, mostly because that one is jealously guarding her virginities so I can explore any future scenes that might specially check for it. *daydreams about a special virginity-loss scene with post-chastity Ryn* Err, right, sorry about that. But that foursome scene is hot.
That does sound really nice, I'd just love if it was even beyond that in customization, being able to switch out their gear and maybe even individual powers. Though that'd get nasty with AI quick I suppose, which is suboptimal.