I expect they were chosen because they affect the greatest number of people. Personally I think the removal of the railroad system in the US was one of our biggest mistakes. Everything is done by truck now but train is actually more efficient from my understanding.

I'm not sure High Speed trains however are efficient. I suppose it depends on how many people are on them. This might be the primary reason only Large metropolitan areas were chosen.

I doubt it has anything to do with actual traffic congestion.

I believe the largest impact will be business. Depending on the cost it could be vastly cheaper to send somebody from Boston to Washington for a day meeting. I would think it would also be faster. Without all checking of bags and waiting for a time slot and waiting to land.

I think what might be more interesting is how well they integrate each of these systems into the local public transportation. If you could do away with renting cars on the other end you could greatly affect the environmental impact.
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I like the Anaheim to San Francisco route. Personally I would like to see a San Diego to Vancouver route, with stops in Anaheim, Fresno, Stockton, Sacramento, Eugene, Portland, and Seattle. The goal would be 20 hours from San Diego to Seattle.
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