That is my main problem with cities in general. You can eliminate pollution, make the city bike- and walk-friendly, reduce crime etc., but living together with tens of thousands of people tends to increase psychological stress. Well at least it increases my level of stress living in a city, but I guess I'm not alone.
Another factor against large cities sounds rather strange, (and I'm not really sure it should be decisive choosing your place of living): resistance to disaster - be it a flood, earthquake or a war. I remember seeing a presentation somewhere from the '50s which recommended developing suburb-like living areas because human casualties would be lower there in case of a nuclear explosion, than in a dense city.
That said I think there are major factors, other than wether you will live near a target if a nuclear war breaks out, or if Gozilla will stomp over your apartment (those monsters just love dense cities :)