Population: the forgotten resource
There was a time when population meant something more than just when your city would level next. A time when it affected more than just how much base taxes a city yielded. Apparently that time has passed. It doesn't mean all that much anymore. Now, you can all but wipe out the population of a city taking it over and it doesn't make much of a difference. Production, Food per grain, research and mana are all created by buildings and base location stats. There may not be any people left in the city, but somehow everything still works just like it did, minus the unrest. How is that exactly? How can a city crank out military units without any affect on its population? And how can a city that you just founded afford to outfit a group of pioneers that can go out and found yet another city?
I think we should return to the idea of units costing population to create, especially pioneers. If building a pioneer reduced your population by 25, how many could you build before there was no one left in the city? And huge armies flowing from your cities could not last forever if your population was reduced by 3x the figure count (9 for party, 15 for group, etc.) Cranking out units would at very least stifle, if not reverse your population growth. Producing quantity over quality would be cheap and quick, but ultimately self defeating because of the population loss involved.
I'm not sure how to penalize the empty level 3-4 city, but it needs to be done as well. Let's make population mean something again.