A quick look at a topographic map of California suggests HSR through the Central Coast would be significantly more expensive, especially the southern half. Moreover, the Central Valley has more than 3x the population and significantly more land available for expansion, presumably in large part because of the topography. Also, I believe there are more Federal forest lands a Central Coast route would have to get through, which in retrospect might have proven a fatal choice.
Paralleling I-5 seems like a much stronger argument, though I'm not sure that would have been better and it may have never gotten off the ground at all. For one thing, Stockton, Fresno, and Bakersfield might not have supported CAHSR if it bypassed them. But also, AFAIU, Federal funding was contingent on following the routes laid out in the national high-speed rail plan drawn up in the 1990s, and the recommended California line went through the big Central Valley cities.
What's really held back CAHSR has been the law suits and related dithering (e.g. environmental reviews more prolonged because of the expected law suits). That sapped momentum, and momentum is everything; time is money. That loss of momentum also means CAHSR is having a much harder time getting over the humps, literally (tunneling through the mountains) and figuratively (financial support for the tunneling). If construction had proceeded as fast as it has in most other countries, people wouldn't be perennially debating the chosen CAHSR route.