An interesting post, with a lot of good suggestions. I've heard some good things about the FrontRunner commuter train, Provo to Ogen. It would be great if the Runner could make a good connection with the Calif. Zephyr, but I think the Zephyr arrival schedules, into Salt Lake City, would need to change.
As far as areas for untapped ridership potential, Marin and Sonoma counties, in Northern Calif, might be a possibility.
We now have a commuter train called SMART (Sonoma-Marin Area Rail Transit), which travels from Larkspur (in Marin county) north to Santa Rosa, CA. (in Sonoma county). SMART will eventually expand to Cloverdale, CA which is the northernmost town in Sonoma county. The only way to use a SMART train to make a linkage to Amtrak is to take a SMART train to the ferry, in Larkspur, to San Francisco and a further connection to Emeryville and the Zephyr station.
There has been a proposal to extend the SMART train from the Novato Hamilton station to Suisun/Fairfield, along highway 37. I'm not sure, but I think there are already tracks in place for such an expansion, although work on the tracks would probably be needed. Suisun/Fairfield is a station stop for the Amtrak Capitol Corridor train. Also, the Cap. Corridor train stops in Davis and Sacramento, with the ability to connect up with the Coast Starlight. The proposed SMART train expansion east, if it comes about, could bring in a lot of potential Amtrak riders from the North Bay area.