Funny that BART got to SJ via the East Bay first, but I hope they make the most of it. This does complete a missing (edit: rail) link around the Bay -- though sadly across three different transit systems.
Some time ago I wrote that the geography of the Bay is unfortunate for transit in many ways [1] but notably because there's no express way to get from one side to the other; instead you have to travel along the Ring touching all stops between.
One of the later plans of the HSR along the Caltrain corridor wants to operate it as a hybrid system (which sounds like a big deal, but really just means operating express and slow trains on the same corridor), which would greatly improve mobility between Downtown SF and SJ, as well as regions adjacent to those with zoned trains. Similarly, the Dumbarton Rail Corridor (between Fremont and Palo Alto) would provide a radial transbay option.