0.11 stuff:
1: The inventory (Especially while interacting with girls) is too small and it quickly becomes a chore to find items in it. The items should really be separated by type or something. You have that whole ass side of the screen to use, why is the window so damn small?
2: Similarly, the build menu becomes obnoxious to navigate with more upgrades. Most of the room types aren't too obvious and making us scroll when it shouldn't even be needed is an odd choice. You could show all the options on that screen easily without scrolling. The names of the rooms should probably be shown without needing to mouseover them as well.
3: You should be able to cycle through your girls from the interaction screen. You have so much unused space on that screen, you could do a lot more with it. Remember, plan on players having like 20+ girls when you're planning this or this game is going to be a pain in the ass to play later on.
4: Balance wise, there should probably be a limit on how many bandages you can use in combat. I would personally separate the healing and the anti bleed effects to two different items as well. Bandages you may want to be able to use multiples of them in a fight, while the healing being used multiple times is too OP. You could maybe have a higher level item do both. It's way too easy to heal characters early game atm.
5: Inspect Character window should display more exact stats, especially Energy level. With a ton of characters, managing them all and keeping track of them is obnoxious. You may also want to add a "favorites" option to allow people to find their favorite characters quickly and allow players to sort by race and by class as well.
6: Random girls asking to join is maybe a bit too common an event atm. I feel like most slaves should be captured instead. I easily end up with more minions than I'll ever reasonably need before I even have a way to reliably capture slaves atm.
7: The research screen doesn't need to be separated that much or have each choice be that large. You could probably easily fit most of that shit in a single window even with future upgrades accounted for. Why did you choose circles for the research screen when most things in the game are squares? It really makes the research screen stand out and feel awkward compared to the rest of the UI elements imo. Might just be me, but it feels like the UI elements in the research screen don't match the rest of the stuff in game, like it was designed for some cheap mobile game or something.
8: The distinction/connection between stats and levels and combat strength isn't really obvious. A level 80 girl can easily lose to a level 20 girl, that makes the level system and stat system completely pointless. You should be able to see an intruder is X level and know that your girl that is 5-10 levels lower will struggle against them. Right now the level of the intruder barely seems to matter basically. Stats don't seem to effect things all that much either, I would prefer more specifics about how those work or it's hard to tell if they're even worth raising.
9: The Farm research option comes a bit late in the research tree, it forces a certain build order, especially if you pick up an additional girl or two at the start. Right now accepting any extra girls is an early game trap to all your girls starving. Unless of course you're no brain spamming gold/research buildings in your first rooms...which is a pretty stupid strategy for a dungeon master, even if it's sort of meta atm with how easy invasions are, lol.
10: I'd like if there was a "collection" job where a girl will go around collecting items from the production sites. She could patrol between 2-5 zones or something if running around the entire dungeon is too much. If it's not going to automatically be collected anymore unless the girl is set to that specific room, something like that should exist. I dunno how intensive that'd be on performance, but a girl only collecting from a single room is a bit weak atm, I thought the girls randomly wandering around would collect but I guess not.
11: Auto eat seems to happen pretty late, girls will often get the hungry debuff in combat if left alone. Might want to allow players to choose when they eat...kinda fits the controlling dungeon lord theme as well. Could do the same for bathing. If it was easier to feed them all quickly, it'd be less of an issue. Well this is a pretty minor thing with a small amount of minions since the Inspect Character window at least shows the hungry debuff, but again, will be a chore with like 20+ since you have to go into each of their interaction screens to feed them atm.
12: Going into the jail/prisoner room and clicking the prisoners one by one is also a bit painful atm, I hope there'll be a quicker way to reach them, like adding them to the Inspection Character window.
Overall the game seems designed for how much content is currently in it, and not often planned out too well for how much content will be in the game. A big one is how painful the game will be when the player has like 20+ minions. Even if you don't plan for people to have that many, they will. This is the kind of game that gives people that "Gotta collect em all" feeling, everything needs to be planned around that or the game will be too obnoxious to play.
I recommend you try to reduce the amount of clicking/time needed in some areas to do things. That's a lot of my UI issues summed up quickly. A good example is how you have to click to open the research options menu dropdown box, scroll down, through the categories then click again to choose a tree. That could be reduced to a one click thing to choose a tree even if you don't want to put them all in one page (Put the categories on the side of the screen?). Similarly, how I recommend trying to get rid of the scrolling stuff when it isn't needed with the build/inventory stuff. You might also want to add a way to feed girls without having to enter their interaction screen. A "Feed all" button might be needed at some point. There are some exceptions, like when finding items would be too difficult without some things sorted into their own tabs. You'd save time in that case by being able to find what you want quicker by tabbing over to a certain item type.