I have seen bits and peaces of ideas like this but not the whole. I would like to design a home like the bog houses.
So adding ladders for level to level travel
Craft able holes (second and third floors only I guess) so you can go down.
divider walls so you can split up a level.
Raise the height of one level.
Jumping platforms (like furniture but more like the mushrooms or hills)
Shadow areas so you can create little hidden nooks and crannies.
Covered areas so the player can walk behind them.
This would not only allow one to match the bog like houses but one could even make ones home into a maze!
Combining a covered area with a divider would create a hidden blocked off area. A covered area with a 1/2 divider would mean someone would have to jump up to get past or think it's a blocked off area.