I have a suggestion. Let us raze conquered cities by default and add a tech tree path that allows factions to keep/maintain cities. This tech path could be researched multiple times to increase the maximum production of the conquered city to 100%.

Tech Name: Occupation* 

Level 1 (Martial Law): +50% Training Time, -50% Gildar Production, -55% Prestige/Population Production

Level 2 (Civil Unrest): +30% Training Time, -30% Gildar Production, -40% Prestige/Population Production

Level 3 (Vocal Protests): +15% Training Time, -15% Gildar Production, -25% Prestige/Population Production

Level 4 (Total Assimilation): +0% Training Time, -0% Gildar Production, -0% Prestige/Population Production

*Note - add/subtract an additional 5% for Empire, may want to introduce some kind of limit to available buildable tiles

After conquering a city, it would be razed or the player would be given the choices to raze/occupy the city. The choice to occupy the city could depend on a few factors:

(1) The player's faction. I feel that the Empire would be more likely to raze.

(2) How far the player researched into the Occupation tech path.

(3) The sovereign's charisma stat. It gives the stat an additional use and seems to make sense.

(4) The distance from the conquering player's capitol. (This one may not work out after testing.)

Since Elemental does not have city flipping, I think this would be a viable alternative. This also gives the side that had just lost a city the opportunity to get the city back. (At this point the city is still contested and its production would be based on how far Occupation had been researched in the tech tree. If Occupation had not been researched, the city should be razed. This would penalize the original player for losing the city in the first place and prevent an opposing player from expanding his/her empire.)