I think the shower/dinner room idea is good but what would the clone character do?
Besides threesome or group sex stuff there is always interesting stuff that could be done. For example besides the drilling how about Dungeon Mining which could have better outcomes the more individuals there are (making the bunk beds a reward to acquire and not make).
I have had some additional thoughts since the last time I typed something up. Additional Rooms (Storage Cart [Visual Representation of all the loot collected], Equipment Cart [Where the Drill, Picks, and such are located], and Entertainment Cart).
Trophies (Acquiring em through Drilling, Winning em in contests, earning em from the Girls, buying em from settlements, and ect..). For example for the Bunny girl maybe a Carrot Lamp that will be placed in her room.
Settlements (Bunny Burrow, The Dragon's Den, and Wolf Clan) Each could be places you can trade for unique stuff, get information, help improve with the resources gathered (must be in the place to do so), and probably other things. Thinking maybe expanding the map a little if you add this.
Clothing taking into account the Roxie Skin for the wolf (which has her wearing clothe) how about making the clothing itself optional for players with a wardrobe in their respective room for players to equip the girls (this also means each Palette being able to wear the same set of clothes [Each girl having their own set of Unique clothes and the clone girls use the clothe of the individual they are copied from but allowing the player to if they want to customize them individually within that set]).
Could we also get a Catgirl the same size to the Kobold (2 or 3 or the palettes could be taken off of Monster Hunter series).
Final Idea and easier one to do. View Flipping. When viewing the vehicle from one side how about being able to flip it to the other side. The reason being while many of the rooms would have a change in perspective (being able to see other things from a different angle) the living quarters don't need to be all that big so the player could have a whole set of quarters that are still untouched.