MORE USES FOR POPULATION!
I don't believe the starting city needs to be the most important city but I do think you should be able to change capitals, and there should be special improvements for capitals.
Also, there needs to be a bonus for population once you reach city level 5. Otherwise what's the point of all those extra prestige buildings? Population needs to modify tax percentage, troop build time and resource throughput more significantly.
Troops should cost more than one population. Maybe the population cost for a troop should be something like cost/5 or /10. Something to represent that a fighting unit requires support staff to function. You know, like a knight might have retainers or something like that. So your dirt cheap peasant might cost 1 pop, whereas a knight with a warhorse, longsword and armor might require 100 pop.
This population would not be "used" as in buildings, but directly removed from the city pool. If you lose that unit,you lost your pop investment.
Finally, Sovs/Champions/NPCs should acquire experience over time when garrisoned in a city. The experience should be proportional to their charisma trait and competitive with running around battling/killing monsters. A character that devotes ALL his stat points to charisma and staying in a city should be the same level as some other character that runs around fighting stuff. Make it so maintaining a high level of charisma would be critical to leveling up at a reasonable rate.