I'm a little surprised that those kind of things are work-intensive, but then I'm not a programmer so don't know how long it takes to put "Kuro was here" on a blackboard, Emica's eyes being different, or posters of Rai Ghoulie.
Regarding the girls, I understand that, world-building can be a challenge and you want to make sure it's not too sparse. Taking Aya as an example. sure she doesn't have much screen time, and you could probably get rid of her with no real change to the story... but you'd miss out on some truly funny moments!