I've played through this game so far and I had a few suggestions although I don't know if you can implement them as I've never made one of these games.
1) A mood meter: I noticed that certain characters don't like doing certain things. I feel like adding a mood meter that increase/decrease when you put them in the right or wrong jobs would be interesting, especially if this leads to special or unlockable scenes with that character or makes them rebel and leave.
2)
Spoiler (click to show/hide):
Age play or bestiality inspired characters. I know not everyone is into this which is why I put it in a spoiler tag, but it is a post apocalyptic world with pretty much no law or governance chances are this could and would happen.
3) More combat situations. Although its not necessary, maybe when you leave the bunker you have to fight off random encounters. Knowing that you have people working in an armory and you're not doing much with the weapons their making kinda hinders the idea.
4) This one could go along with my first idea, but I was thinking that each room (armory, lab, ect) ends up having it own sex scene added. Such as in the lab where food is being created, maybe you end up with a mutated plant that or in the maintenance wing, someone decided to fix up an old robot that turns out to a "pleasure droid". Things of that nature.
Hope these suggestion weren't an overstep. I know you have a lot to work on already, just like the game and want to see it get even better.