Tool tips when you mouse-over an element are on the to-do list.
Not keen on variable undo. Undo is a bad reward. It's the wrong message - for being good at something you are treated like you are bad at it. If you carry on being good then the undos are worthless. Undo is for learning. I will likely add the option to turn it off, but definitely not a mechanic to get it back.
Levels are never generated on top of each other because the code requires to the rooms to be separate for a lot of mechanics to work. Duplicating a room as part of a level progression might be an idea though.
There are no trains - they are implicit due to the HOOK passive (press P to open the editor during a game). There is only a single layer of data, no floor, no sky. This rules out a lot of cool things like jumping over stuff and pressure pads. Maybe something could take away passive abilities like HOOK and WALL - but it would be very boring with no passive abilities around. Or maybe it could trade them - unsure what would be good. Ideally I'd like to be able to do an ally and enemy version, unlike the scroll tile which doesn't really work for enemies.
The level state doesn't keep a record of previous turns (the undo stack is just a pile of level states). So time travel isn't possible. The level data is simple and clean and must stay that way. If we had an enemy that changes state over time, then we could target that property. That's probably something that needs to be made - an element that switches behaviours.