Structures
I don’t really like the idea of water mills. It would be better to keep the sockets as the exclusive domain of Trading Posts. A resource trickle is also a pretty uninteresting bonus. Even the new mills could be made more interesting if they had more functionality or interactivity. For example, they could require a food investment similar to Lombards but just yielding a greater quantity of food (they could even remain under your control for the duration that you have food invested). A global boost to farming yield as you suggest could also be an interesting way to make them relevant in the late game.
For other structures, I’d like to see more impactful and game-altering properties. Villages could provide this kind of impact.
Villages that increase the population cap and also provide housing could appear on Chinese maps.
Fishing Villages that provide a gather boost aura and act as an infinite source of fish could appear across Southeast Asian maps.
Bridges could be another interesting structure. Capturing them could give you sight lines over river crossings and give you the option of demolishing a bridge to eliminate a river crossing and restrict land mobility or expand naval mobility. They could even be as simple as pontoon bridges that could be reconstructed by boats.
A structure that generates natural resources could also be useful. Something like a Buffalo Pound could generate bison. For this structure, I’d prefer it be a building for Lakota and Cree (if they ever get added).
Treasures
Treasures where the guardian is the treasure. The wild boar on European maps gives food when killed so this is already kind of a thing. This could be taken farther with things like bull elephant guardians being harvestable for their ivory, or bears that could have their pelts gathered for coin. Essentially something similar to how the AoE4 boar works. The corpse of the guardian could become the treasure that is to be gathered, and the gathering could be done gradually like how crates are gathered instead of instantly as it is now.
Some treasures could also be guarding natural resources such as black bears guarding a blueberry bush.
Natural Resources
More natural resource types would be an improvement. However, for emerald mines, I don’t think they should be infinite. Giving experience in addition to coin would be a compelling enough difference.
Some other natural resource sources could be as follows:
Dens - Limited source of coin. Gathering upgraded by hunting upgrades
Spice Plants - Source of coin. Gathering upgraded by berry picking upgrades
Quarries - Source of ‘wood’. Gathering upgraded by mining upgrades. This could increase the available wood on arctic and desert maps without ruining their aesthetic by filling them with trees.