I'm glad you put "natural" in quotes to show that it's your word and not mine. Sure: call it an "engineering problem" -- it's still a problem that is (and has been) solved better by a highway with trucks than some spectacular rail line that's only useful for freight.
Look at it this way: even given a blank check, the good "engineering solutions" for west coast rail all go through the central valley (i.e., away from the coast) ... just like I-5 did 40 years ago. Which means you immediately lose the benefit that everyone is so charmed by in Europe: downtown train stations.
Don't get me wrong: I'm not anti-train. I like trains. But it's just not going to work to revisit the original
As for the "50 years ago we had good transport" I can say that transport only got good in the Bay Area when they built the Bay Bridge, and the train that runs under the bay (BART) has far more capacity than the Key Line et al ever did; yet the spectacular growth of this area would still have dwarfed the capacity of rail lines.
/jordan