Formality typically rules a large settlement. There are laws, regulations, police, a legal system, mayors, voting (in free societies), zoning, and even procedures like how to evacuate or handle certain emergencies. Everything is taken more seriously due to physical and population size and diversity. Otherwise, the chaos overwhelms, especially in times of conflict. This formality can become a problem, however, when groups are marginalized or taken advantage of, or when laws and regulations are unfairly and inconsistently applied, causing social strife that may boil over into protests, riots, and death. Congestion also makes the spreading of disease an issue. Cities offer the best and arguably worst of everything due to competition and quality.
The population is likely to be diverse even if some wish this were not so. Even hundreds of years after a settlement began, newer species can face racism from factions that want a return to the old ways, when their majority ruled and made no concessions to other species. A stark difference between poor and rich can be common, and stricter separation of crime-ridden slums and clean, wealthy districts is common. Marginalized groups will have less sway in town affairs and may be prevented from holding office.
Cities may have the best fortifications and military to staff them, with entire garrisons of trained warriors, many with elite skills; formal ranks are likely and a subculture for these people will exist, with inns, taverns, and equipment shops catering to them. All of this is more likely with somewhat isolated cities as found hundreds of years ago; such places weren’t yet surrounded by suburbs, and police, not military, enforce daily order and the military is reserved for civil unrest and actual wars or excursions into other territories, for example.
Zoning will prevent industrial, commercial, or residential from mixing but will result in more traffic from commuting, even if that’s mostly pedestrian in fantasy settings. Such a scenario lends itself to pickpockets and people hawking wares to passersby, making for noise. Main thoroughfares are more likely to be paved; otherwise, the mess after a rain storm is considerable. In SF, all roads are probably paved and parking is another concern, though public transportation may have reduced or eliminated this.
Pollution is a major concern and taxes help pay for better infrastructure to minimize the risk of illness spreading. Sanitization is generally better unless the city is run down. Increased anonymity in the largest cities means people only know a small percentage of the population and can fall back on stereotypes and prejudice to judge those nameless masses with whom they share a city.
Rivers and lakes provide the needed water for cities, so we’ll want to place our largest settlements along them, though in SF we can use technology to create drinkable water from sea water, for example, and make better use of irrigation and the divergence of rivers from their natural course. Dams can also create lakes that didn’t exist before. There are also likely man-made reservoirs, particularly if the area lacks water.
In SF, public transportation is common and might include a space port. We should decide where this is located, but the answer is that it’s typically near industrial areas and somewhat out of the way due to pollution, traffic, and noise; think of airports and all they provide in food, other transportation, and nearby lodging.
The largest type of city, sometimes called a metropolis, is so large that it has often absorbed nearby villages and even entire towns. Individual towns may have retained their names and governments, but physically they’ve been absorbed into the metropolis, with no intervening gaps. These formerly independent settlements could have building styles unique to them and seem like neighborhoods of the larger settlement. If they had walls, those might still be there because in an attack, each walled area has its own fortifications.