By order of importance, there's a couple of things i see missing in this game.
- "wand selection" just like photoshop or any other editing software, it would be great to select a shape with selection
- "mask" selection already acts as an inverted mask. I think it should be the opposite, you should only be able to edit inside of the selection, not outside, and it should be so for wand selection as well. You could also just be able to apply a colored layer of a mask to prevent editing in that area temporarily, without taking up the selection forever.
- Paste function, have a small clipboard for pasting things, because going up and down floors doesn't work with copy.
- Floor transparency. Instead of needing to hole everything and build on top, have an option to tune the opacity of the current floor and the one above too.
- Having terrain change with a button would be nice, like water to lava, waterfall to lavafall etc.
- Reverse animation for some items, like a reverse Waterfall where you can climb it with flippers.