The San Francisco Municipal Transportation Agency oversees the city proper’s surface transportation network, including bike lanes, public transit, traffic, parking and taxis. But it carries less than half of the region’s trips. Commuters traveling by public transportation from the East Bay to Mountain View or other Silicon Valley locations face a train ride and at least three buses — a connection possible only if everything is on time.

And demand has grown for these services. The traffic lull that occurred after the dot-com bust is long gone. In 2014, drivers wasted an average of 78 hours of delays in traffic, with San Francisco and San Jose ranking among the top five worst cites in the United States for traffic, said Jim Bak, a director of Inrix, a transportation data and analysis company in Kirkland, Wash.

Ridership on CalTrain is up by 10 percent, for example, “a reflection of the economy and the appeal of San Francisco,” said Art Guzzetti, vice president for policy at the American Public Transportation Association in Washington, D.C.

Still, only about 10 percent of Bay Area commuters take public transportation, Mr. Rentschler said. The ascendance of the so-called Google buses, which ferry workers from various tech companies between far-flung suburban campuses and their neighborhoods in and around San Francisco and have drawn criticism from residents, underscores the need for a more efficient system, according to SPUR.

Even transit operators agree that transfer points like Embarcadero Station in downtown San Francisco “are the places where we should be doubling down,” said Tilly Chang, executive director of the San Francisco County Transportation Authority, which oversees long-term planning and administers funding. The authority is working with BART on a rewards program that would coax riders into traveling during nonpeak hours either by offering points on electronic payment cards or luring them with prizes, like coupons from local businesses.

Though certainly preferable to clogged highways, stations like Embarcadero test the mettle of even the most intrepid commuter. There, a transfer from BART to the city’s light rail, known as MUNI, requires negotiating two levels, exiting through a turnstile, paying a new fare, entering another turnstile and descending another flight of stairs to reach a different platform.