Regarding using the Pioneer Tunnel to improve the ability to move more trains through Cascade Tunnel, see this earlier post regarding BNSF cooperating with the UoW in establishing a laboratory in Pioneer Tunnel.
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I know that sounds crazy, but there is a link to a letter from Matt Rose of BNSF saying they were supportive of the project!
The big plus to BNSF would be that the pioneer tunnel would be improved at (state expense) and allow better/increased/improved ventilation of the main bore of Cascade Tunnel.
The BNSF letter is dated 2007, but I am not aware that anything concrete has come of this project.