You're gonna kill me for it, but...
Multilevel undo.
If an editor lacks it, it's either "save rarely, then after many hours of work realize you screwed up something and your last save is from yesterday", or "save after every click, and not realize you just saved broken version".
Been there.
Besides that, well... you definitely want to avoid 1-pixel (and other small) holes you would get stuck in or fall through, so you definitely should have a mode that highlights the "floors", and preferably either warn you about, or quietly "fill in" such tiny gaps.
Now, if you're asking about things that are feasible to code... I don't have any.
Best of luck!