San Francisco runs from the Embarcadero waterfront west to the Pacific. Union Square is on BART and Muni. The Wharf is where the Alcatraz boats leave, with bay walks on the doorstep. The Mission gives up the postcard views for restaurants and murals.
Union Square has Powell Street BART, the cable cars and a long list of hotels. You can walk to Chinatown and North Beach, but the hills make short distances on the map feel longer. The Financial District and the Ferry Building are farther down Market Street, on the Embarcadero.
At Fisherman’s Wharf, PIER 39, the waterfront walks and the Alcatraz departure piers are close together. The F Market & Wharves streetcar runs along the Embarcadero to downtown. A Wharf hotel suits a first day on the water. The Mission and Golden Gate Park are a longer transit ride away.
In the Mission, BART stops at 16th Street and 24th Street, with trains to downtown and SFO. You stay here for the murals and for eating and drinking around Valencia Street and Dolores Park. Hayes Valley, near Civic Center, has smaller streets and its own restaurants. SoMa makes sense if you are going to Moscone Center or Oracle Park.
The de Young Museum and the California Academy of Sciences are in Golden Gate Park. The Presidio and the Golden Gate Bridge are farther north. In summer, fog and wind can make a waterfront afternoon colder than the inland Bay Area, so carry a layer even when the forecast looks mild.