Very true.

A direct route along 99 would take out the centers of several small towns, with community impacts and costs related to that but little or no possibility of service (call Amtrak or Greyhound for frequent stops). Going down I-5 (after getting over/through the Coast Range by one of several possible routes) would be faster between the Bay Area and LA but would ignore everything in between - perhaps appropriate for Hyperloop which is intended for the "flyover" traffic, but less so for something intended for mass transportation.

Yes, the flames will begin, because everybody has their own opinion about how stupid this or that decision is or was. So be it. Yes, there are compromises. For something oriented at providing transportation for actual people, they are necessary.