I'm surprised that the Coast Starlight has not been cleared yet to go to Vancouver. It seems like a no brainer to have train service from Los Angeles to Vancouver.
In the post September 11 era, crossing the border has become much more of an ordeal than it was in the past. There also may not be enough through passengers to justify the added expense of operating an additional train only two hours prior to a scheduled "Cascades" to or from Vancouver.
Several reasons. The first is that it doesn't fit the schedule. The train would have to leave Vancouver at 5:35 AM and would arrive at Vancouver at 12:12 AM. For an endpoint, that is rediculous. Note that the Coast Starlight also does not serve San Diego. A Thruway bus is offered to Vancouver.
The second is the border. It used to be that the second Cascades round trip turned at Bellingham to avoid the border. It was extended during the 2010 Winter Olympics but every year or so there is a big battle to fund the train over the border, since Canadian Customs requires that Washington State fund the inspection. It is unclear who would pay for the inspection since the Coast Starlight is not state supported.
Finally, the Bellingham Sub is approaching capacity, and doesn't need another passenger train.
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