Steve brings up several good points. The Pt. Defiance line between the current Amtrak Station in Tacoma and Nisqually has only 4 or 5 grade crossings ( Old Town Tacoma, Titlow Beach, 2 in Steilacoom, any others ???), and is mostly double track. The Lakeview Sub has a dozen or more grade crossings, several of which are quite busy ( North Ft. Lewis & Gravelly Lake Rd. ). The line is single track with 3 dispatcher-controlled sidings that I know of; two of these are at the South Tacoma and Freighthouse Square stations. The Lakeview Sub also has the steep climb Southbound from Freighthouse Square up to Nalley Valley, which would preclude any fast running.
I too wonder how much behind-the-scenes influence BNSF is exerting on this route change. BNSF has been doing a great job of giving preference to Amtrak on the Pt. Defiance line; I will often see a freight or even two waiting along Ruston Way for a Cascades to clear the tunnels. Keep in mind also that the Pt. Defiance line hosts EwePee freights as well. Often times I will hear on my scanner that BNSF will not take a S/B EwePee freight @ Reservation "... until after Amtrak. "