Thanks for the update :-)
In the meanwhile, I have finished a game with custom settings (70% mission probability / 5 days repay interval). I think I found my ideal setting, it was really challenging in the beginning (failed to repay once), starting from midgame with having several higher level Captains and some Majors, it got easy again. Btw., are you planning to nerv mid- to endgame a little bit or is your current focus just on writing?
Morale was a constant challenge until the endgame, where I can recover morale by relocating without mission, which is often better than taking a low profit mission in this stage of the game. Normally, the morale situation gets easier already in midgame, but this time I had a lot of stern female officers, and the arranged dates can cost you a lot of morale in the late game. When you add the higher level obligations, which primarily effect the late game, the current morale settings could fit really well.
VIP scenes: Are there any differences in the personalities of the VIPs (expect fo the introduction)? I couldn't recognize any, and they were quite similar to the normal cargo loading scenes. I was hoping for more distinct scenes, and more specific reaction to the current outfit. But maybe I missed something.
Btw., the "Captains are always busy" rule is - against my expectations - really great. It greatly improves the value of locations with only 2 Captains in the early game, as you no longer have to fear that you do not get any mission at all.