The bigger issue is that the freight companies control line maintenance. The upshot is that there’s no incentive to straighten the tracks to run them at higher than freight train speeds.

For example, on the San Jose <-> Oakland commuter line (which has existed for decades!), Amtrak runs trains with top speeds of 120mph (or was it 85?) at something closer to a top speed of 45mph.

Edit: Also, the freight line routes no longer make sense. For instance, they run through a pedestrian plaza in Jack London square to an ecological restoration area in south bay, where most factories have been shut down. (There are still salt ponds, but that salt evaporation plant is slowly being shut down in an ecologically responsible way, as I understand it).

I think they should give the freight company imminent domain rights to run a line due east (to sparsely populated areas), allowing the freight lines to run unimpeded by Bay Area rush hour and pedestrians. In exchange, the freight lines would give their existing right of way to commuter rail systems.

Also, while I’m dreaming, Bart would be converted to standard track width, and they’d restore the Palo Alto to Santa Cruz commuter rail lines. Then, all the systems would be put under a single authority, and all the transfers between the existing systems would be timed transfers.