First off, y.v., it's great to hear back from you! We are all looking forward to the next game update. Unfortunately, the longer you stay out, the more time you have to think up things to add to the front end of the game to facilitate later quests and plot twists. A complete restart for the first several updates is annoying, but not uncommon. ( just don't try to compete with Summertime Saga or Witch Silver Trainer in that category, . . . )
I don't know if any of the sex with other crew members is truly transactional. With Tris, it seems like she's on the cusp of her own sexual awakening. After living in a society that repressed sexuality and other emotions in favor of logic, she's been cut off from her civilization with it's constant reinforcement to conform and it's echo chamber of supposed superiority. Tris is coming out of her shell.
Vee is in a similar situation. She has been cut off from the Swarm hive mind and put into a humanoid shell with all of the biological sensory inputs inherent thereof. She isn't just emerging from her shell, Vee is evolving into her own independent lifeform. ( Speaking of shells, I'm surprised that Nimhe hasn't closely studied the Vee construct and developed a psuedo Vee shell, maybe with some 7of9 flourishes, . . . )
I think you pegged Dr. Moira right with the MILF/Cougar persona. Now you just need to throw in some kinkyness! Get the MC to strip down and run a "thorough?" physical exam. "Accidentally" spill her drink on him and insist on getting him into the shower to assist him in getting washed. Playing "mommy" and breastfeeding the MC. Several cosplay scenarios such as taking him for a "pet walk" in Krell space, MC in a cowsuit and the good doctor as a milkmaid, MC in a Godzilla outfit and Dr Moira ering a miniature of Tokyo costume, ( Thank Phil Foglio & Dixie for that idea)
Khelara appears to have an exhibitionist streak in her. Once they reopen the exercise, health and fitness unit, I can see Khelara continuing to workout in the altogether and inviting the MC to join her. There can be massage/masseuse opportnities in the gym too. (Maybe Tris can join them?) Khelara will still insist on being compensated for wearing a revealing uniform, but when she's on her own time, she is self confident enough to wear or not wear whatever she damn well chooses!
I think that Ylyee should be added as a Passenger/Crew member by order of the Voron Council as an Ambassador/Science Consultant as the ship ventures into little known space. Payment to the ship could be in the form of a ship upgrade to say Infernium Plated armor. She already accepted exotic dancing in the Itari system as a way of competing her mission. It would be interesting to see what else she's willing to do.
Seraphine has already shown an inclination to be a submissive while on the holodeck. That needs to be explored further. She's already shown herself to be an overprotected, spoiled brat, . . . maybe some "Daddy" issues?
Nimhe has already shown that she's into bondage and ponyplay, both of which have yet to be properly explored. What other fetishes is she going to diplay next? ( I'm voting for WAM and nyotaimori, . . . )
We've already spoken about Verity being a trouble magnet and popping up as a recurring DID. Of course she will have to properly reward her rescuer.
All of the females on board are strong personalities in their own individual rights. I think you have it right in that they are all not going to fall passionately in lust with the MC, (except maybe Seraphine). I think it much more likely that they would discuss it amongst themselves and decide to make him their boytoy and conspire to let him think that he's in charge. At least until his personal sexbot obtains more memory cubes, . . .