You ask for a lot of things without giving much reasoning. Yes, the things you suggest would add a lot of colour to the game but do they add any depth? How would your proposed additions impact on the game? Think about these things when making suggestions, and be careful not to just ask for bigger and better versions of what already exists without explaining exactly what it is you want to change and your reasons why you think this is important.
Two ideas I will focus on because they stood out to me: permanent/replenishing resources, and animating garrisoned buildings.
Animated buildings I think is a great idea, a very nice, intuitive visual indicator that a building is garrisoned.
Permanent/Replenishing Resources, you argue that fish stocks and forests regenerate in real life so why not in game? What purpose does it serve to try to emulate real life? Does this serve the game? This is not a good reason to promote an idea, be careful asking for realism or you might get what you wish for and will have to organise the disposal of all your 2000 citizens poop! Instead ask how it affects the game to have finite resources versus infinite resources, and try to determine which option makes for the best game. One problem is that with infinite resources the game could potentially never end. With infinite resources the issue of supply would change from quantities of resources to rates of harvesting, how would this be imposed upon the player? For example, perhaps the more you fish a certain fish stock the slower it regenerates. What about maturity? Maybe it takes time for new trees to grow and replace the ones you cut down, perhaps aggressively cutting down a forest of mature trees would even help younger trees to grow faster in the open space? So forests could have the opposite replenishment behaviour to fish, the more depleted they become the faster they replenish.
You see how I am thinking about how the game works first, then drifting off into ideas that echo the real world, then pulling back to try and adjust these ideas to fit into the game and see how we could, in a simple way, get some of the feeling of those real world ideas without needed to simulate them completely?
I hope you do not think I am being patronising. I give this advice because I see you are full of ideas but I think your ideas could use a little direction.