CAHSR essentially consists of 6 separate pieces: Bay Area-to-Central Valley; the SF Peninsula run; Sacramento-to-Central Valley; LA-to-Central Valley; LA-to-San Diego; and the Central Valley itself. San Diego, San Francisco, and Sacramento were all planned to be later phases anyways, which means the initial operating segment choices are either the Central Valley itself or crossing into it in the Bay Area or LA.

The Central Valley was chosen as the first construction package area because a lot of the initial money CAHSR got from the federal government had to be spent quickly, and flat ground means that the construction would be the cheapest and quickest construction portion. That the result has neither been cheap nor quick is a pretty severe indictment of the epic mismanagement involved.

It's also politically astute to do the first major public spending in the reddest part of the state, and then connect to the endpoints who are less likely to change their minds.