Mopping up is a tedious thing and every 4x game suffers from it. The AI seems to be building a LOT of cities. Would it be an idea to have the sovereign only escape to cities that have some sort of prerequisite building? I remember in AoW you could only escape to a city with a mage tower and these things were expensive to build. Erecting it in your first city should be a given, since that city is built by the sovereign itself.
Makes the game more strategic and city spamming a little less interesting.