Finally, somebody who knows something about game economics
You cities automatically allocate enough farmers to feed your population and armies (meaning the more armies you have, the more farmers you need, the less workers you have and the slower your production is)
That was a problem in the original MOM, you constantly needed to adjust your workers and your farmers to make sure you have enough food to maintain your army while not wasting people doing extra farming. I am not sure how well an automatic system would be, maybe the food cost will be shared between cities. In MOM, most of the time, new cities farmer were kept low to increase production and the high level cities were maintaining food. So I am not sure how efficient will be the automatic system.
Although it never hits the point where more Unrest means less gold (higher taxes always give more money),
That was also a problem in MOM, raising your tax too much and you were actually losing resources. So what happened in the end is that you set you tax to a fixed level and keep it for the whole game. You could add the option to add tax reduction for specific cities. Because when you have a lot of cities, some cities will be able to handle the unrest while others won't. It could be a way to temporarily accelerate the growth of a city. Second, you want to give the players a reason to have low taxes, else they will just raise the tax until there is no unrest. My suggestion is that having low tax to a point where no unrest is generated could give extra bonus somewhere else. A quick suggestion could be that it raises the research level or population growth, etc.
Another point, adjusting sliders in a turn based game is not fun. This is what happened in MOO3. Because there is not any real decision taken. You simply adjust your rate until you reach balance. I have a suggestion where maybe you get a budget report at the end of the year, or X turns that tells you how much income you received and what were your expenses. At this point, you can decide to set up the taxes, and give tax cut to specific cities. Then you need to wait a whole year be fore changing tax again. This gives to the player more decisions, to I raise my taxes now or wait another year.
You could always have an emmergency tax or offer the player to pillage their own city to take the missing resources, but it increase your city unrest of course.
Another thing, in order to have the possibility for cities to rebel, maybe special events, unrest and pillage increase a "Discontent people" meter that stays permanently. It can be reduces with buildings and with happy people with time. That level would increase or decrease every turn. Espionage actions would raise the ennemy's discontent level. When the level reach the maximum the city rebel it self. A war is taking place between militia relative to population level, and the garissoned unit. If the militia wins, the city revert neutral. Militia killed reduce population of course.
Tile yields don’t extend as the city extends, they are only those 9 tiles.
So you only harvest a 3x3 grid and building over these tiles "destroy" the yield?
When a city is taken in combat half of its population is lost.
This is just too much considering also that killing soldiers somewhat kill population. I would say at most 1/4th of population which could be reduced at let say 1/8th with city walls, but not more.
fixed build times are gone
This is one feature that I found interesting, because in MOM, you always had this problem where because you did not have any population or production bonus, a building could take 60 turns to build, and then if you add 2 workers, it takes 8 turns. So there was a high difference in the production time and cost of the buildings. Same thing for units.
unlimited improvements are gone (you can never make more than 1 of an improvement in a city).
This is another feature I found interesting because it allowed player to creatively design their cities. Maybe not unlimited, but maybe 2-3 copies of each building. Else in MOM, and other 4X games, it feels more like working, you need to build everything because there is no interest in not building everything. So there is not really any decision in city development, just build everything. Still, you specialized building idea, which looks nice, it adds some decisions. Another solution I proposed for a mod is to reduce the amount of buildings you can build. If there is more buildings to build that the number that can be built, players will need to do a choice which building to build.