It is a city, by literally all definitions. Nearly 900,000 people live here, making it the second densest city in the United States. So there's a lot here to be found if you bother to look for it, or just generally know how to navigate a city.
Perhaps if you are coming here to conduct commerce and nothing else it will just feel like... a place to conduct commerce! But that's something you can say about every financial district in the world. The places that have "soul" are almost never the places dominated by office towers.
Don't get me wrong, SF has many, many serious problems. Not being a city is not among them.