An easy to implement feature
It's a universal truth that any feature described as "easy to implement" is no such thing. That being said, I'd like to do more with structure adjacency. Like an irrigation system that boosts the output of adjacent farms, or docks that require adjacent water.
a system for multiple structure layers
I'm not sure how multiple structure layers would work from a UI perspective, or how useful it would be. The "building on swamp" case could be handled by having a worker unit that could fill in shallow water(changing it to grass or dirt). Siege engines could also be done without layers, they wouldn't work well as structures to begin with, as structures are assumed to be owned by whoever owns the territory (i.e. the town you're attacking).
there should be a way to set certain resources to be visible only to certain races in the UI
I have a note on the issue tracker around item based progression. The idea behind that is to hide certain things until the player has discovered the items they require. E.x. the player wouldn't see the option to construct a bronze statue until they have discovered bronze. And they wouldn't see the option to construct a bronze smelter until they've discovered tin and copper. This would have the side effect of hiding items that a race can't use. Masklings would never see copper in their UI because they have no way to obtain it.
a quick build bar of some kind to settlements / hold shift to place multiple
That's a good idea, I'll see what I can do.
Thanks for the suggestions!