Just throwing in some more ideas:
Cities:
Creating a settler cost 1 citizen and require the city to have X amount of stored food (stored food can be traded between cities and civs)
Cities take some turns to settle, and start out with really low defense
City growth rate doesn't slow down with higher population
Military & workers:
Military units and workers created from citizens
Military costs and workers costs food to maintain, equal to citizens
Earlygame units can be build in a set number of turns regardless of production, while lategame military units take a minimum number of turns to make, but also rely on production and may take much longer if the city has low production output
Military units and workers can be converted back to regular citizens
When a city is taken in conquest, all defensive building are destroyed (I'm actually not sure if this is already a feature)
Technology and science:
Techs can have specific requirements: sailing require a city at the coast, iron working require source of iron near a city
Science no longer based on population size
Culture:
Rather than unlocking social policies, culture is the base for tourism
Tourism provide money, and other civs will take a contentness hit for starting a war with you if you have a lot of visitors from that civ
Contentness:
Replaces happiness. Low contentness cause rebellion and less military effectiveness, rather than slowed growth
After discovering currency you have the ability to tax the people of your empire, higher tax give more money, but less contentness
Spawned rebels reduce city population, can take control over entire cities, rebels can either be killed by the military or you can make a deal with them to make them stop
Contentness add to golden age counter like happiness used to
Another idea is arming the people, which cost some money per pop, and increase city defense, but also make rebels more dangerous. Then if you want to disarm the people, you could move military units into cities to search and disarm by force (killing some citizens and damaging the military unit, reducing contentness), or use money on a no-gun campaign, which only work when the people are fairly content, removing all their guns after some time
People from other civs may emigrate to other civs with a higher contentness
Resources:
Strategic resources more important for cities: example, factories could boost production/economic output +50% each, making coal supply very important. Iron allows building a steel mill, +20 production etc... Bring on the resource wars.
Cities can produce consumer goods as a luxury resource that only lasts temporarily