Problems:
1. what happens when I capture a city?
maybe the population of the city don't mind a switching of rulers but surely all the mages, royalty, training instructors and governing bodies are scattered or destroyed... so how are the labs still functioning?
2. What about when I found a tiny settlement in the middle of a wasteland? instantly have random students, technicians and teachers flock to your new labs and training instructors magically appear in your baracks? No... you need "logistics", a simplification of the administration in place...
Rather than both free and usable tiles be based on city level, have the functioning tiles component be determined by a logistics resource. So logistics lv 2 provides city lv 2 worth of functioning tiles. You can still build that city in the wasteland, make labs and facillities but they will not function until you can send the appropriate people to actually run them (not just the workers driving the pumps, turning the wheels and carrying the materials but the teachers, master smiths and inn keepers ordering them around)
For it to work have a building with exponentially increasing cost of upgrades providing logistics equal to 1 city level's worth of functioning tiles per upgrade... Building a new logistics building costs as much as an upgrade to the first logistics building and gives the same number of tiles as an upgrade would. Therefore having one logistics building in each city costs the same as a single building upgraded the same number of times supporting the entire empire. The choice is merely in having all your eggs in one basket or spread out - useful for targetting by city spells but a juicy target.
These logistics points (administrators, technicians, mages, teachers etc.) would be local to the city but shared with any city with a connection (road+caravan).
Logistics could also be used as a global resource with appropriate high power spells/races/traits to enable it - e.g. enchanted caravans, mental dominion +x global logistics or simply switch local to global (the global bonus only used after the local logistics are used, for supporting newly captured cities/settlements) for a lower power level spell (magical control, enchanted road, etc) it could be cast directly on individual cities to boost local logistics
An Austrin style civ favouring distant colonies could have some form of wavering of the rules... either have no connection requirement for the first x logistics drawn from the capital but increased costs/reduced tiles per upgrade... or better still that could be achieved by having something similar to a 'prepare expedition' order, costing as much as an upgrade but making the next captured city/founded settlement have a free logistics building placed on creation. Further a military civ could have units providing a few points of logistics to the stationed city, e.g. taskmasters, slave drivers, psionics (+2 logistics, -1 prestige per unit in city with a production boost if logistics are unused... causing the city to shrink with too many active at first (negative prestige for turning them into slaves))
The idea's just based on a modified sins of a solar empire theme... also I would suggest only non-housing buildings be non-functional without appropriate logistics support... so towns still grow, they just don't produce anything useful... so you'd need to protect your logistic hub(s) and newly captured or founded cities wouldn't have any logistics buildings or connections, requiring either building local logistics or connecting them to allow them to start producing resources and units. A lack of logistics wouldn't stop people settling there or cause everyone to flee, but it would stop the city growing faster from prestige buildings. I think it's better than "angry unrest/rebellion/discontent" to explain the time it takes to get a captured city functioning, plus it would happen in stages for a large capital... it'd take 5 upgrades for a lv 5 city to become fully integrated into your empire, unless you've prepared for the conquest and have the logistics in place and magically create a connection, have slavedrivers pour into the city and make the population slaves or capture the city while not damaging any logistics infrastructure. All of which give extra possibilities while requiring some advanced tactics or enabling some special civ traits.
Another concept here would be that certain traits could be linked to a building types logistics cost, a military race would have military buildings not require logistics (or half cost) as anyone can run them - everyone is trained in combat... a magical empire wouldn't require logistics for certain magical buildings and a farming race wouldn't require anyone special to show them how to plant crops. So civ traits would make each race have very different settlements... at least the smallest settlements with only a single building. And almost all cities would have a building or two of the civ's speciality as they're free/cheaper to support.
Anyway... any thoughts?
I'm not sure of having it being like sins in planet upgrades or fleet logistics... since it would make it less of a no-brainer if there was an associated upkeep cost increasing with each upgrade, afterall all those greedy high-ups should require wages or a piece of the pie. But I prefer the soft(er)-cap of exponentially increasing upgrade costs... although having the upgrade and upkeep costs increase in a more linear manner could allow for faster early expansion for some and have upkeep techs be the capping device for city spamming.
e.g.1=75, 2=150, 3=300, 4=600, 5=1200, 6=2400 v.s. 1=100, 2=200, 3=300 -3% upkeep, 4=400 -6%, 5=500 -9%, 6=600 -12%...
With these upkeep costs/upgrade costs reduced one level by each logistics tech, also outright boosts to logistics provided by spells... so you would naturally expand even as a small empire as your tech increases and an early rush would require a period of teching afterwards to reduce the potentially crippling upkeep of logistics support... possibly leaving you vulnerable as you would have the output of a smaller empire until you catch up (determined by how much you stretch your power)