Wow, now that would be an ambitious RTS type of game. Doing a game like the one you are proposing here is a huge undertaking but I really really like your ideas of a real "RTS" with real elements like the weather.
Maybe with enough development time you can add that different interactions between settlers to make it more "real".
One idea that has been in my mind is about some kind of "level up" for villagers (citizens) so if you put one to mine he gains experience and get to do it faster as time passes, but if you put it to gather lumber then the XP gets reset and starts again slow gaining XP but for lumbering and so on.
Thank you for taking the time to post your ideas on a genre that sometimes seems now a little lost in the shuffle.
There are other elements I have in mind actually, but too many and too complex to explain. Such as the moonlight that reveal a ghostly secret path for shortcut or surprise attack, or a path to a hidden resource. Or natural creatures that attack all sides which could be used against your enemy, etc.
I didn't think of villagers levelling like that and damn, it sounds like a great idea! It's logically correct. I'm thinking of putting some powerful units on guard to keep a high-leveled miner safe from the enemy because it would be a shame if that particular worker die lol.
And thank you for stopping by. If you're into RTS too, you might want to check out the two RTS I mentioned above.