It would be nice to see tunnels built for the 101 freeway through San Francisco. Maybe one day. One can dream.
I'm not sure it would save that much. The fastest way from San Jose or parts south to San Rafael and parts north is NOT through San Francisco, and would not be even if there were a tunnel connecting 101. On days when the weather is decent, the traffic delay over the Golden Gate Bridge is not from the bridge's capacity, or the cross traffic on 19th Avenue or Park Presidio Blvd., but the right lane of the bridge being backed up all the way to Golden Gate Park with traffic for the Bridge visitor's parking lot.
The undeveloped parts of the Bay Area have had a strong "humans are the virus" mentality since the 1970s and have opposed any infrastructure projects (freeways, 4 lane highways, aqueducts) that might possibly allow more people into their bucolic wonderland.
And I'm glad they did, so they Bay Area has a few miles of suburbs alternating with woods or park or agricultural land. Partly due to keeping down road construction, but other measures as well: zoning, parks, ownership by the Nature Conservancy and similar organizations. Without them it would be 10,000 square miles of unrelieved subdivisions with no open space for play and native plants and animals without driving for hours.