So I capture a city, and then magically all its inhabitants become members of my kingdom. I think that doesn't feel well.

That people came to the city atracted to the former sovereign, and they are loyal to him, not to the new sovereign. Their loyalty should stay with that sovereign, and should not stay in the city.

Maybe some of them will stay in the city no matter who governs it because they don't want to become nomads again, but the rest should come back to the wild unknown world and/or go to another city if the losing kingdom still have any city left.

To make things simple, let's say that:

• If that was the last city in the empire:
  • A random number between 0% and 33% of the city population become loyal to the new owner. That number could be affected by some techs and/or by some sovereign skills (both the old and the new owner factions)
  • A small random number between 0% and 5% of the popualtion (again modified by techs and skills of both factions) become soldiers loyal to the attacked faction and appear just in front of the city. They have low quality weapons and the lowest experience level.
  • The rest of the population just dissapears. They come back the wilderness.
• If there are more cities in the empire
  • A random number between 0% and 33% of the city population become loyal to the new owner. That number could be affected by some techs and/or by some sovereign skills (both the old and the new owner factions)
  • A small random number between 0% and 5% of the popualtion (again modified by techs and skills of both factions) become soldiers loyal to the attacked faction and appear just in front of the city. They have low quality weapons and the lowest experience level.
  • A random number between 0% and 25% of population migrate to another city in the empire. They appear in the map as a unit heading to their destiny city
  • The rest of the population just dissapears. They come back the wilderness.