Short version, I hate them, quite possibly in totality. I'm sure there's something I like about them, but I have no clue what it is at the moment.
First, the attempt at limiting them via food. Miserable failure. The only thing limiting city expansion is money. You can build a garden, thus a house, thus hit tier 2, thus having research, income and production of all sorts. You have another location to run caravans, another location to produce troops from, another location to gain population. Even if fisheries were eliminated, it would still be the case. With fisheries there, as long as you have lots of coastal cities, you're even spamming large ones.
Getting tanked by a couple hundred coin on the other hand is quite the deterrent. Which is annoying. You can't build a large empire instead of a small one. What happened to the open environment? Where is my trade off between having a powerful Sovereign or a powerful civilization? The answer is nowhere.
Second, cities themselves are incomparably lame. I used to hate the way Civ was set up with the lame access building system, but this is so much worse. It's like civ, without building terrain improvements. The design of the city is meaningless, what you build in the city is meaningless. They all end up almost exactly the same, someone in a persistent vegetative state could build one just as well.
Established points, the food mechanic utterly fails, the monetary pile driver makes every empire roughly the same in size, and the building system is about as interesting as a dentist appointment.
Solution, fix food, get rid of the silly soft cap nonsense.
Sticking to the "resource" model, fishies should be a resource. A fishery should use a fishy resource. No fishies, no fisheries. More than one fishies, more than one fishery. Continuity in mechanics is important.
Get rid of this idiotic one building of a type per settlement system. It's completely devoid of a single redeeming point. This isn't the modern age with fertilizers, most of the civilization is going to be farming. Your ability to produce should be dependent on those left over peons that aren't busy trying to feed themselves. How you use it should be up to you, not some silly one per settlement restriction. A city with no food source should take everything up just to increase the population.
Set costs to building a pioneer much higher, resources to build housing, food through the winter. Include a much higher population cost as well. People don't come from nowhere after all, in return, start them out with more than one population to match the cost.
Disconnect "farming" from the fertile land resource. You know what you grow in shitty ground? Shitty crops. You can still grow food in less than perfect soil. Assuming an expenditure of essence to make land fertile, you simply balance food production below zero use out of a settlement working infertile land to feed itself. Simply amassing cities will then lead to a high population of farmers that can't produce anything else to fund your war efforts.
Populations will now soft cap themselves based on how much work you put into them and what resources you acquire. No "one garden" nonsense required. The population levels suck too, but I'd much rather the suck fest mechanics are fixed than I get to keep using them with a million people instead of a thousand...
Now we get into wishful thinking, things that would be better but I don't expect to happen. Get rid of food and housing construction. It's trivial, it's pointless. You might as well "train" each peasant that's born as micromanage where they're building their housing and farming.
How to do it in a non trivial way that isn't pointless? Automate it, ditch the "food resource" system too. If you build next to fertile land, where do you think the peasants would end up farming? People are stupid, but not that stupid. You start your settlement, begin building things that are of relevance and value to you as the Sovereign. Your peasants handle their own lives. They go out and build houses, start farming, naturally ignoring any demands you make of them unless they can do basic things like eat. Civilization only exists when people aren't starving. When they are, you have bloodshed.
So, you stick a settlement next to fertile ground, your 10-20 peasants, however many you've stuck with pioneers, get to work. Your settlement has a production capability of zero until there are peasants producing excess food that can switch themselves off after finishing their housing. If this settlement is one devoid of productive methods of gaining food, that means never unless you set up trade routes and have excess production somewhere else to get shifted over.
End result, cities that can be geared towards specific tasks, expansion of production controlled by aquisition and creation of resources, no tacky limitations, and, with the latter automated farming and housing, less mind numbing clicks towards the mundane.
I loath the way access and stationing is done in cities as well, but that's more for another subject once tactical combat is added.