Someone on Robert Cruikshank's CA HSR blog, I think, posted a link to the Amtrak Capitol vision plan:
CCJPA Vision Plan, What the Capitol Corridor Can Become
The overarching goal is a modern railroad built to international standards, electrified and capable of top speeds of 150 miles per hour. This could reduce travel times between Sacramento and Oakland to just over an hour, and between Oakland and San Jose to a half-hour. This plan also envisions a direct connection to BART in central Oakland, just minutes from San Francisco.
Volume 1 was done in 2014, and volume 2 in 2016. The plan lists a rather severe challenge: much of the Capitol Corridor's route is not very high above sea level, and also very close to San Francisco Bay and San Pablo Bay. That makes it vulnerable to sea-level rise and storm surges. The trackage through Suisun Marsh is affected by subsidience, something that is already a maintenance problem.
Between San Jose and Fremont are two routes: the Coast Subdivision near the Bay, and the Warm Springs Subdivision more inland, both ex-SP. There is an east-west connection, the Niles Cutoff, between the two routes in Fremont, one that extends further eastward to Pleasanton, Livermore, Tracy, and Stockton. The Coast Subdivision continues further northward to the Oakland Coliseum, and from the Warm Springs Subdivision, the Niles (ex-SP) and the Oakland (ex-WP) Subdivisions continue more inland to that stadium. The ex-WP route from Milpitas to San Jose is now abandoned, and BART is being built on it.
The Capitol Corridor trains currently do Coast - Niles Cutoff - Niles, but it could be rerouted all Coast, Warm Springs - Niles, or Coast - Niles Cutoff - Oakland.
In downtown Oakland, they considered grade-separating the route through Jack London Square, and also bypassing JLS a bit to the north along 5th St., and also a tunnel from east of JLS to near Emeryville. The second option would include a station shared with BART at West Oakland, and the third one a station near BART's 19th St. station. The third one would also be very expensive for only 3.5 mi of route.
Oakland to Richmond is very cramped, with no good alternatives to the existing right of way.
Between Richmond and Suisun City / Fairfield, they considered several routes. They dropped a route through Vallejo and another one along I-80, leaving the existing route and a route in Franklin Canyon. The existing route would be straightened as much as is feasible, raised, and expanded for additional tracks. The Franklin Canyon route would follow a BNSF route and then enter and exit State Route 4 with tunnels, ending up at Martinez. These two alternatives both cross the Carquinez Strait, and an additional bridge would be constructed for it, high enough to let ships pass under it unobstructed. The existing bridge has a center span that is raised for passing ships, causing scheduling problems.
Between Suisun and Sacramento is some straight track on flatland, but coexistence with freight traffic is a barrier to service increase. The authors propose rebuilding the now-abandoned Sacramento Northern right of way and adding a bridge just east of Suisun Bay that would connect with the Tracy Subdivision.