(on a side note. Did the AI break in beta 3? It was much better at sending armies at me during war in 0.87. Now the AI declares war and do nothing)

As it is now getting an extra city is always a good thing, and this leads to city spamming. I have a few suggestions to reduce the spam.

Toughen up your staring area:

1. Make the low end monster a little tougher. The orges, trolls, mites and spiders are a bit on the weak side, making it easy for the sov (and maybe a champ) to steamroll.

Slow down spamming directly:

2. Producing a pioneer could cost 10 population

Reward larger cities:

3. As a city level up it should get specialists that gives extra bonuses. The type of city should influence what specialist you get. Levelling up to level 4 could give a researcher (+5 research a turn), engineer (+10 production a turn), hunter (+30 food in city), a captain (+1 level to all troops produced)++++

On levelling up to Level 5 you get another specialist. There could be some rare random ones as well. 

Random level up goodies:

1. Your grand city has attracted a superior warrior that wants to join your expanding empire. (get a great unit for free)

2. The superior empire of <EmpireName> is growing and a beast trainer has settled in your city. You can now train up to 6 Ogres in your cities.

3. People are seeing your grand plan, and are flocking to your empire. +50 population in your city.

4. A new engineer has settled in your city. You can now produce units with crossbows.

5. The shopkeeper is getting new wares from all over the world to your great city. He now sells new excotic products in his/her shop.

6. A group of sellswords now live in your city (two units of swordmen will help city militia on defending the city)

++++

Make larger cities defend themselves better:

A rich and sprawling city could afford to equip their militia better. Levelling up cities should make the militia now only increase in numbers, but also get some better equipment or better stats in general.

Make buildings, resources and terrain work together:

There should be more buildings that gives bonuses if you have the proper mix. A jeweller that makes rings for the shop at level 4 or higher city. The rings quality is dependant on your number of shards of each type. The properties of the rings ALSO increase based on the number of jewellers in your empire. So and empire with many shards and three large cities with jewellers would be able to make some really good stuff. 

Just some random ideas here. Feel free to shoot them down