The biggest inconsistency in the pro-HSR camp is the idea that it will connect the suburban communities, and therefore create jobs etc. As many others have correctly pointed out, there is NO WAY that the promoted trip time of 2:40 can occur in any other mode than express (no stops). The only way I can see to rationalize this conflict is to have express and non-express trains. This (probably) may require extra local trackage and systems. Certain areas may have to have 4-track mains to allow express trains to completely bypass the multi-stop trains that will INEVITABLY be wanted by all of the towns in proximity to the line. And the supporters are pandering to this market by extolling all of the "virtues" of the line without explanation or regard that maximum track speed cannot be maintained in an area where there are "puddle jumpers" operating on the same track. Having said all of that, I do support the current proposal of temporary modification to "blended mode". It will have to be well understood that even with improvements to Metrolink and Caltrain, it will not be possible to meet the 2:40 during the period of blended operations.
I think a central core of 225 mph line, with improvements in the urban segments to 90-125 mph will still yield a system that is marketable, although temporaily longer in trip time than advertised. The HSR project is still worth doing as an investment in the future of sane transportation.