I didn't read over every suggestion that has ever been made, so I'm hoping there's not too much overlap here.
In another thread I read, I saw someone have a suggestion for a university that could unlock new spells/buildings/upgrades, which I think is an awesome idea, though I had some thoughts on a different way it could be used. I've noticed right now there's no real system for unlocks/research and I couldn't find a roadmap of planned future changes past the current world map update, so I don't know if you're intending to ever add unlock mechanics. If not (or perhaps in addition to the other idea), the university could be used to boost the intelligence of villagers (especially children) based on the level of the teacher. The elderly would automatically become teachers and the building would have an option to automatically "draft" any villagers above a certain level into becoming a teacher.
So this would be a way to boost intelligence, but villagers also have strength and dexterity stats. It would be cool to have some sort of exercise/gym building that would boost the strength of the villagers who go there and also some sort of building (training center? I'm not sure what Dexterity affects in the game) for dexterity.
There was also a suggestion in another thread for villagers to have a place of worship, which could influence how much influence the player has and maybe influence regeneration rate. It could also have a high resistance to corruption (based on workers/attendance) and boost the corruption resistance in a fairly large radius, making churches a strong late-game tool to combat the spread of corruption and perhaps drive it back entirely.
All of these ideas have a single unifying theme: they do not involve villagers performing "labor". So far villagers seem content to work 24/7 at their assigned tasks, which probably shouldn't make them very happy. They don't spend much time at their homes with their families (though they certainly find time to make those families), sleeping, or just relaxing from the stresses of the day. I'm thinking it would be interesting to add a "leisure time" mechanic. The player would be able to adjust how much laborers work: the default setting would have most workers begin their jobs during the morning and end them at evening. During dawn and dusk, they may go to the worship building, the gym, or other "leisure" building (playhouse? Museum? Carnival?). At night, they return to their homes to sleep and refill their energy. During hectic periods where lots of work needs to be done, the hours can be increased, but workers will have lower energy and lose happiness. If the player is in a comfortable spot and just waiting for population growth or something, the work hours can be reduced, resulting in increased happiness and more opportunity for mating. The exception to the typical hours would be guards, who are active through the night.
From a technical standpoint, having all the non-guard villagers be in houses (assuming they aren't homeless, of course) during the night would free up system resources to handle the monster hordes and general insanity of combat, especially after the first year when things get especially hectic.
In order to help workers stay efficient at later stages of the game, you could introduce a few new building types. The first would be a carpenter who creates wheelbarrows/carts that can be used by villagers to transport large quantities of goods much faster. The second would be a new upgrade level to the farm: ranch. If a rancher finds wild animals on the field (cows, horses, chickens, sheep, etc.) they can be brought to a ranch. Each ranch can only hold a limited number of animals (and would produce much less, if any, crops); they will give birth randomly (some breed faster than others) and if the building's population limit has been reached, an adult of that species will be turned into a large amount of food. Chickens will produce food over time (eggs), cows can produce milk (water if you don't want to add a new drink type), and sheep would produce wool (a more consistent alternative to silk). The last would be a stable, which would store horses and carts. The stable would add organizer slots to the village; organizers can use horse-drawn carriages to transport large quantities of goods quickly, freeing up harvesters to continue harvesting instead of collecting and distributing resources and saving construction time as builders would not need to spend as much time bringing resources to the site. Both carts and carriages would move EXTREMELY slowly on unpaved ground, making them almost less efficient than just having a worker carry resources, but increased road levels will give them a high boost to their rate of speed.
The last ideas I had were for two more buildings. A prospector's office would allow you to hire prospectors who will search the buildable radius around the village for hidden resources (iron, gold, underground water sources for higher-yield wells, new resources you could add in the future). Once those resources are found, the prospector will mark them. Then a mine, well, or other building you might add in the future can be constructed to harvest those resources. This would replace the random drops of iron and gold that come from rock harvesting. Collecting resources from a mine would be a fairly slow process, but would provide a consistent source of the material rather than relying on random chance.
Lastly, I'd like to suggest some minor building tweaks. I have 11 people crammed into each of my houses. This seems excessive. I think 8 would be a better, more realistic max population for a fully-upgraded house. Farms seem perfect so far; each one gives me four slots for farmers, so I've had to build about ten of them to keep my food supplies up. I feel like harvesting centers should work in a similar manner (four workers per building at maximum upgrade level). I have a fully upgraded castle and a small number of ancillaries and I can't figure out what to do with all my building slots and the space I have for construction. Adding in some new buildings and encouraging the player to build more of the ones that are currently already in place will give all those building slots more purpose, add to the late game challenge, and keep the balance between simulation, RTS, and tower defense as the player begins to fight back against the corruption.
I'm really enjoying Rise to Ruins so far (I've been playing for about two weeks). I'm still learning the mechanics on Traditional mode before moving to survival, but even on traditional, the enemy hordes are putting up a good fight by the summer of my second year. I'm really excited to continue playing and seeing where you take this game; it's awesome so far and it looks like it's only going to get better