1: It would be more realistic to have other ways of making the invaders and such serve than asking them how they are over and over again or buying things to gift them. I understand the kindness factor, but it needs something a bit darker to even it out, especially for those that want to do an evil aligned playthrough. Yes, the zombie route works a little bit for that, but breaking their spirit or keeping them in line through fear would fit as well, without rendering them a zombie.
2: Having the ability to select the player character's learned abilites when interacting with the girls themselves would also be something to look into. It's a little irritating when you get a new servant that you want to interact with, only to have to wait for the shop to be selling the book with the desired position or method to teach them. I understand that you can interact with the player character themselves in order to accomplish this, but with the huge number of servants you have at later stages, finding the right one in the list again can get tedious.
3: Having the ability to actually do something other than watching an invader walking around aimlessly in your base would not go un-noticed. Currently, you either have to just let them wander as they please, or spend coin to banish them temporarily. Being able to dispatch servants to intercept the invader, or being able to move the player character between rooms to intercept them personally would be much more engaging. This would also open up the ability to introduce more than one invader at a time, and make it more like a tower defense or rts style game.
4: Have the ability to keep track of learned recipes in crafting and alchemy would be a huge bonus. Keeping a list of recipes open on a second screen isn't possible for everyone, so being able to scroll through a list of learned potions or items to see what ingredients they require would be helpful. The list could also be used to automatically input the proper ingredients into the alchemy interface.
5: Adding a help tab. When I first installed, I was completely lost on everything due to not knowing any controls, or what buttons on the screen did what. I was almost an hour in before I figured out the combat system is not only attached to the characters themselves, but also the weapons they are carrying, and in a few minor cases, their other equipment. I still don't know if the player character can actually move into another room without physically moving the throne room itself.