I agree, I would be gutted to see the city types disappear overnight for the next release.
I think upkeep and sprawl spam are actually not that big of a problem needing that big of a solution.
We already have the seed of some good solutions, scaling upkeep with empire size would be a great addition to really get that cooking!
Ok so my playthrough is stuck so I will type here instead!
I think the big problem with city spamming right now is that:
1. There isn't really any kind of expansion penalty. (Except the risk of over extended defences and angering natives till they attack.)
2. You get 'Everything you need' free everytime you build a settlement. A production facility and resources to feed that production facility. A monastery gets a free research facility, etc. Add to that a few technologies that give buildings everywhere and why wouldn't you city spam, monastery or otherwise.
3. Settlers and cities are free, so by converting a peasant to a settler (free) and founding a city (free) you get a new produced good source (free).
4. Pop Limit. With the pop caps in place (not a bad system) you have to build buildings to expand your city, that take time and investment, where you could just build a new free city with free production slots. So you are given many reason to grow wide, but growing tall is not easy (shouldn't be) and there is not that much to gain by focussing people in a single place. (except ease of defence, which is a good reason, but not really enough).
5. Limiting the free rewards. I think if we just reduced what you get for free when you build a city, or make deeper use of the 'prepared' of settler types, so you only get the free stuff if you use loads of wood and food and tools, etc. It would reduce some of the draw of spamming new settlements.
Perhaps if starting buildings only have 1 worker slot and only produce 1-2 output, while the next level has 2 or 3 slots and produces 3 yield, that would make a town 3 or more times as effective/efficient as a village.
So sending out a man to build a village will only give you 1 produced yield, where as working him in a town will produce 3. This makes villages far more 'rural' in nature, where the only decent work is working the land. This would reduce the desirability of spam, as you would only get raw materials (that don't bring much at market) and having to network and transport over a larger area.
6. Monastic Spam/The City Type Ratio:
Right now I think the monastery is the most obviously rewarding city type as it gives you a free research building, and a boost to livestock, ale, wine and crosses(with a shrine). I think the town and outpost just need some more identity maybe, or the monastery needs to be a bit lesss instantly awesome.
Perhaps towns could start with a boost to raw materials, food and such, so that pairing a town and a monastery works nicely. Town feeds grapes or barley to a Monastery and a Monastery feeds those back to town and on to trade sites.
We could take more buildings away from monasteries, such as anything but a basic dock, the ability to build ships, the ability to build warehouses(or large ones) so you have to move their products fast, to town sites for storage, most (if not all) high end production buildings.
They could recieve negatives to many resources, so that they are only good for 6? Resources (Cattle, Sheep, Wine, Beer, Crosses, Candles.)
We could change the plot group city type bonus to be much smaller on a per city basis, with a cap of say 25% with each producing 5% so that you want to make an even amount of each to get the full bonus, rather than just building say 1 out post to get the 25% fealty boost or whatever.