In beta 4, a new city system has been introduced. The major changes: 1) Essence has been introduced, 2) buildings can be upgraded, 3) city specialization and 4) re-balance.
1) Essence: the new Essence resource is a nice improvement. The problem is that Essence is very strong, and important to both Fortress and Conclave cities, with low effect on Towns. Also, a problem it posses is that the more Essence you have, the more each Essence is worth. Empires with high level casters will want to buff Fortresses with buffs to trained units, Conclaves are balanced around high Essence in the city, while Towns receive only the basic enchantments of growth, research and such. This turns certain tiles (ones with low Essence) into obvious Town cities, instead of a hard choice between 3 options (with obvious preferences).
2) Upgrading buildings is a nice improvement. I personally like that that I no longer have banana cities running around the map.
3) City specialization: Also a nice improvement, letting the player to further specialize. You could go further with it in level 3, 4 and 5, though. Instead of a small buff at level 3, a city could further specialize: for example, a Fortress in level 3 could decide whether he wants to create stronger troops, opening better/cheaper buildings that improve them, become a more defensive city (bonus defenders/stats, some of them faction wide), or become a "prison" (increased influence and -unrest Empire wide).
Note: the level-up screen is still problematic, as we can't really see the city, only in the background. The city info window should be opened immediately, allowing the player a bit more information before his choice.
4) Currently in FE, there are two issues that bug me, one is the population, and the other is production:
population: In 9.5 I noticed that population do not increase research and production anymore (might've been in an earlier version, or maybe from elemental, but now I noticed). With armies taking quite a few people from the cities, the cities grow and grow, till they get to the max population cap, and continue growing once you increase their food supplies.
Currently, population is a problem, as it requires a lot of effort game wide for no reason.
We get very little from population:
1) Gilder from taxes: Is not really needed, as we got buildings that give us that amount. In my games, unless I wished to waste money on rushing buildings or buying champions, Gilder had little use (no upkeep issues due to buildings supplying money)
2) City levels: at certain amount of population cities would level up and give a 1 out of 3 choices of "pimp me up".
While we spend on population:
Buildings that give happiness, food, prestige, growth.
A chunk of our cities that goes to be Towns, whose biggest advantage is faction wide food increase.
Research to make all this possible.
A 3rd of our resources (grain) goes to to increase the population.
Certain spells go to affect our population.
In the current meta-game, we could scrap the whole idea of population, give cities an adjustable timer for growth, and have a nearly identical game, only better (easier to learn & manage).
The production is in a much better state than the population, but:
1) There are currently 2 ways to get production- materials, which in some city are scarce, and Enchantments which requires Essence.
2) Capped production per city. In FE, there is an issue with producing too much- you can only build something once every 3 turns, no more. So even with a high amount of production, creating a meager scout will take 3 turns, as much as the Ironclad Knights. This is very counter-intuitive, and frustrating.
Either a player doesn't have enough production to build what he wishes (and lets remember we can't decide which city builds the improvement), or he is frustrated that he can't use it. This brings us back to Elemental, when we had a set amount of turns per building... only now it can get higher if we have low production.
I personally believe that a city should build with all her production- the first item, then the second, till either it used up its production or the queue is empty. (This was done in Endless Space quite well)
One more thing: Defense versus Attack- what is the math, exactly? I still see creatures with lower attack than my defense easily hit an armored target for 1/2 per creature in the stack.