OK, now we're thinking of doing a circle trip, Emeryville to Chicago, then Chicago to Seattle, then Seattle to San Jose. I think those routes are the CZ, EB, CS, right? Is either direction better? We are also waiting on family availability, so are flexible on dates. Trip of a lifetime!!!!
Both choices could make a wonderful trip. I like to choose based on scenery, particularly the Mountain sections.
You can download a current System Timetable on-line at
https://www.amtrak.com/ccurl/294/1015/Amtrak-System-Timetable-Winter-Spring-2016-rev.pdf
On page 79 of this publication is a map showing which sections of the Western Routes will be in daytime, if the Train is on time.
The Coast Starlight looks better northbound, for daylight between the Oregon Border and Eugene. This stretch may be dark southbound.
The Empire Builder looks better eastbound, for daylight crossing the Cascades. This stretch may be dark westbound except for the final section.
The Zephyr looks as good both ways on the map, so we consider possible delays.
Westbound, we leave Denver around 8 AM for a great view climbing into the Rockies. If a little later, no problem.
Eastbound, we arrive in Denver around 6:30 PM. If the train is delayed very much, the best part of the Rockies will be in the dark.
The Sierra Nevada are very likely to be in daylight in both directions, even with moderate delays.
So my preference based on seeing the Mountains by daylight would be: Bay Area, Seattle, Chicago, and Bay Area, taking this wonderful Loop Trip in the Clockwise direction.
Enjoy!