The missing roof piece (triangle to finish a peaked roof) really bugs me. It feels off to leave a hole there. Spend aged trying to fit everything possible in that hole.
Agreed on vertical half walls. When building random shaped enclosures in the woods, especially near objects like juice boxes, it would be nice to be able to add an extra grass plank to patch a hole. Or allow the walls to overlap with objects would be fine too.
Dyes and half stairs would be awesome too. I like to build 1.5 storey houses because one floor height makes rooms feel too claustrophobic and low. Seems like a waste of materials to make double storey rooms just to add room height, but it's impossible to make the stairs work with half storeys. Stretching the wall pieces to taller proportions would also work. I don't know code so no idea how hard that would be to make.