Cities suck right now. Not constructive feedback, I realize, but there you go.
A long, long time ago during the Elemental beta, it was pitched that Cities would be unique constructs, each specialized with different special bonuses unique to that city, with choices in their development that would allow you to tailor them to suit a particular role.
I would very much like to see that, whatever the actual execution is.
So, current issues:
The entire building placement system is useless and needs to be scrapped or totally revamped.
Currently, buildings don't involve any meaningful choices. With a handful of exceptions, you build everything in every city, and there's not even a way to automate what is essentially a mindless process. Basic production boosters -> growth boosters -> remaining production boosters -> food boosters/research boosters -> anything else you need.
Without interesting decisions, building up cities is boring, and building up new cities in the lategame, a chore - there isn't even a build governor system to automate the buildup, which could be handled with a short list of build plans - boring.
The core systems in place for cities are totally solid - the core prestige/maintenence/gold/research/growth/food/unrest systems are clean, simple to understand, and work just fine - but they're also automated systems with no meaningful player impact on their development. The widgets you have available are 'what do I research' 'what is my tax rate' and 'what order do I build buildings in the city'. That's it.
In and of itself that's not bad, but research unlocks very few structures (and is too slow by default, a separate but related issue), the tax rate is typically too harsh of a swing towards gold or research/prod to be used in the early game and by the midgame its nearly irrelevant. The buildings involve little to no decision making.
The level ups are one of the few unique systems in place, I think that system should be developed and expanded - instead of a single building each level, transform the the level-ups into a branching system that lets you customize the city to your needs. One path gives you troops with unique abilities, another unlocks advanced research that is otherwise inaccessable via the tech tree, another path unlocks special magic, either spells or items, another tree unlocks monster related bonuses, another tree specializes in hero upgrades, etcetc.
Unique structures rewarded for quests, awarded (or gifted!) via diplomacy, researched, or discovered in the wilderness. Once unlocked, these could be built like the (few) 'wonders' in the research tree. Each would provide a unique benefit to a city, on top of whatever city development branches you've built up. You could potentially gift unique plans to an ally for a significant diplomacy boost and a useful ally in war, or recieve them in exchange for diplomatic missions or trade. The Tree of Life (trade its seeds to allies!), Warmage College (train special caster units), Titan Essence (create unique demonic creatures that cause a diplomacy penalty), Elemental Shrine (unlock special spells for one element), etcetc.
Some unique structures could also give *abilities* to the city, allowing you to cast special spells, summon up temporary armies/units within your territories, create or modify items, and so on. How about a unique structure that gives one city two build queues? The Tower of Storms, The Manaforge, The Golem Factory, etcetc.
There is already a very vestigal form of this in the game, with the rewards for killing the unique wilderness bosses (this entire concept is very cool, incidentally), but it could be vastly expanded, enhancing the richness of every game and the unique nature of your cities.
Some of those levelup rewards and structures could also be racially unique, giving more differentiation between what are currently bland faction differences.
Another addition would be *units* that are 'civilian', rather than military. Currently there are pioneers and caravans (which need to be excised entirely). I personally hated worker management with a passion in Civ and Civ style games, as it was early game busywork and mid-late game drudgery, but that doesn't mean FE couldn't use unique civ units to do cool things with cities.
Great leaders that you station in a city providing bonuses, but that could be captured if the city is raided (not razed, that concept needs to go, cities are too big an investment to poof in one turn). Researchers recovered from enslavement in the wilderness, heroes who agree to join your cause from quest rewards that train your troops in special techniques, and so on.
They could possibly even be designed such that they have abilities with cooldowns that provide bonuses, so you have to move them around your empire and actively use their abilities to provide their bonuses, be they simple/boring % boosts to some output, or more interesting special bonuses (unique unit creation, ability augmentation on created troops, special structure construction, unusual spells, etc).
This would also be a role that 'Admin' heroes could be merged with, as currently they have a few boring passive bonuses for sitting in a city and that's it.
Terrain is another untapped resource. This is used to a light extent by docks/lumbermills, but it could be vastly expanded. The presence of rivers, hills, forests, mountains, and special resources - beyond gold/crystal, but unique resources that provide for special weapons and armor to outfit troops from that city, or unique resources used to power certain types of spells. This would give much more interest to placing cities, and make developing them a real pleasure (it would also give another unique differentiation between a small/large city empire and a large/small city empire - one lets you exploit resources more fully, another gives you access to more types of resources).
These ideas are all off the cuff, but any/all/more of them would be welcome over the current system.
The unique structures and units are also something that could be a target for city raids, it would be interesting to be able to attack and damage an enemy city without simply capturing it wholesale - strike to destroy a key structure (temporarily?), steal plans to build your own, or capture an enemy civic leader. It'd add another aspect to warfare beyond 'capture/raze everything in sight'. It could also give another diplomatic goal, something you could ask for in trade, threaten to destroy, or ask an ally to destroy or capture.
Another thought is that when a city is outfitted with a unique structure, some of its build options could be to power the ability of that structure - so now you have lots of things to do with cities - you can a) Build a structure Build a unique structure c) Build a unit d) Upgrade a unit, hero, item e) Craft an item, f) Power a special ability. A lot better than 'this building gives you +20% gold for an EMPTY build queue' why give rewards for doing nothing and not making a choice? How boring is that?
Whatever systems are chosen, special city bonuses and units need to be transparent to all players.
It is vitally important that if an AI player has a special city with a unique structure, or unique civic units present, that you can see that information easily in the ui, so that you can make informed decisions about who to ally with, who to fight, and what cities to target for raiding, to destroy key structures or capture key civic leaders.
This is a sin that many, many 4x games are guilty of, but shining a clear light on _what_ is producing those dangerous units for one AI, or where they are getting a large chunk of their gold/research/production/etc from, or what cities are developed with dangerous unique buildings makes for more interesting gameplay.
Tangental, but I actually think that starting the game in a black fogged world is a bad idea in these sorts of games, because your decisions are limited to 'explore randomly', it's not until the midgame when you have discovered the lay of the land that you can make more interesting strategic decisions about who and what to fight, where to explore or defend, etc.
So in brief:
Current system is functional but boring.
Add customized city development.
Add unique city development rewards.
Add unique structures.
Add unique civic units.
Add unique terrain effects.
Consider adding the ability to raid and pillage/steal/capture unique structures/bonuses/units.