Transit in the Bay Area has very fragmented governance: 27 different transit agencies for 7.6m people in 9 counties with little coordination and no regional vision. By most measures, the Bay Area has the most fragmented public transit network in the country. See Seamless Bay Area if you want to make your voice heard for fixing this: https://www.seamlessbayarea.org/

For a map and list of the organizational insanity, see https://www.seamlessbayarea.org/blog/transitagencieslist (2019).

(Large tech companies like Google, Meta, Apple avoid all this by using private employee-only shuttles which take the freeway where possible).

BART from the East Bay is in the process of being extended to downtown SJ (latest estimate: "2036", they are still debating single-bore vs twin-bore tunnel, to save money in construction).

It's not fair to just blame BART vs Caltrain though, there are multiple cities that need to cooperate with other too: as we saw in the neverending saga of the CA High-Speed Rail project, people wanted a midpeninsula stop, but no midpeninsula city (Redwood City vs Palo Alto vs Mountain View) wanted to be the one to incur the increased traffic and enormous construction disruption from underground multistorey parking lots, so it was dropped.

At least, Caltrain electrification is finally promised, fall 2024: https://www.caltrain.com/projects/electrification/project-be... (more reliable (=> fewer breakdowns and delays), less noise, cleaner air quality)

They still haven't finished that leg? I was there 7 years ago and the plan was advertised on the maps.

You can get to San Jose on BART now but have to go all the way under and around the bay instead of directly south, so it’s not really worth it to go from SF to SJ using anything other than Caltrain.