Where to start? I spent 6 years in the early planning of this thing. This after 9 years on the Taiwan High Speed Rail seeing it go from a line on the map to riding the trains. I will say some things here that I would probably not or at least think twice about, but chances are I will never work again. There were several of us that had been involved extensively in Taiwan that came to California that had long experience in passenger rail, but we were not listened to as much as we would have been had not the French have been invited to the party early on by the state. I am firmly convinced that you can say the most ridiculous things in the railroad world with a French or German accent and people will fall all over themselves to believe you even if you don't know a thing beyond "This is the way we do it [wherever they are from]. Meanwhile those of us that had real experience in more than one way of doing things were ignored because we spoke with varying American regional accents. (Tiawan started off with German and French in their DBOM contract so we learned much of how they do things, but thanks primarily to financial issues they were asked to go away. They were replaced by JARTS (Japanese Railway Technical Services) so that Taiwan ended up with Shinkansen track, trainsets, power, control systems. With that, many of us learned much of how things were done on the Japanese Shinkansen system, and thanks to their constant meticulous analysis over the years they had developed solutions to many issues the Europeans were not even aware of. Remember, when they started, 200 km/hr = 125 mph was considered the edge of the planet for speeds on rails. Not true and most of the more recently built Shinkansen lines are designed for and operated at higher speeds. In fact, the Taiwan HSR trains ran 300 km/hr = 186 mph extremely smoothly. This was not just due to equipment, but also some attention to alignment details unknown in Europe. (At least these did get plugged into the California Alignment Standards.)
As several have said, there was a huge run up in costs following original estimates. These estimates were done by the state DOT, not those in the Consulting Engineering group doing the basic standards and planning. There is a joke that runs like, State DOT estimates are what the job would cost if it was being built in Heaven. Another is, for the job to be built at reasonable cost without much being modified or given multiple useless additions, you must first shoot all the politicians. After a couple of years into the planning process we were wondering whether this should be a joke or a plan. An outstanding California example was the replacement of the eastern half of the San Francisco Bay bridge. I do not remember the exact numbers, but I think the original estimate was on the order of 2.1 billion and the final cost something on the order of 4 billion, and yes that is BILLION with a B. For this they did not get one lane of additional capacity, and having supposedly gotten significant cost saving by eliminating the "Buy America" clause for the materials. And, by the way, all real and imaginary deficiencies and seismic damages on the original bridge could have been corrected for probably one percent of that.
Savings by reducing the design speed? NOPE. Lower speeds on the ends were already in the plan. The difference between 180 mph, 200 mph, 220 mph, 250 mph for most of the route is near zero. First, a straight line has no inherent speed limit, and much of the line in the valley is relatively straight. Allowed maximum grade is 3.5%, but for the most part keeping the grade under 3.0% could be done without being more costly. The alignment design speed was for initial operating at 220 mph, without precluding later speed increase to 250 mph. That was achieved in the design standards and to the best of my knowledge throughout the final alignment, again excluding near the ends. Likewise, Pacheco Pass and Bakersfield to Palmdale could be designed to the highest of the speed limits with little to no cost over the lower limits.
Two things were strongly recommended but slapped down. First, that the entire Central Valley portion be built elevated. Any extra cost would be minimal because it one fell swoop that eliminates all the cross alignment access issues, road grade separation issues, wildlife crossing issues and trespassing. Along with that that the entire line be built with a non-ballasted track form which has several significant advantages. Again any extra cost would be minimal, and on elevated structures more than overcome by reduced design dead weight in the structure and simplifies maintenance significantly throughout. This is just a brief outline of its advantages. If you have seen any pictures of the early TGV trains, the train looks like it is surrounded by a cloud of dust. That is because the aerodynamic forces pick up the small stones and dust in the ballast. The faster you go the worse is this issue.
I quit for now.