I have only lived for extensive periods of time in two cities: SF (2 years about) and Philadelphia (4 years). The biggest difference between them is that even in some of the worst areas of Philadelphia in terms of drug crime, there were far fewer people actively dealing or doing drugs on the streets in large groups. It was more spread out—there were issues in all areas of the city, but there was no area with the sheer concentration of say the Tenderloin or SOMA. There were basically no differences in terms of the transit systems—I don’t think BART or MUNI are any worse than SEPTA.