The trip was a 94th birthday present for FIL. What else do you get a guy who pretty much already has everything? 
We travel a lot, but he doesn’t. MIL died 3 years ago and he lives alone. When they were younger they had planned on traveling in retirement, but then she decided she didn’t want to, so…
Due to health issues he’s not comfortable on long car trips. Due to loving to watch an airplane “crash” series of some sort on TV he didn’t want to fly. Amtrak came to mind after H and I took a similar trip last year.
We planned it all ourselves, though Amtrak offers vacation packages for folks not wanting to put it together themselves.
We showed FIL the route map here (train in red, bus in green) and asked him what he’d like to see along any of the routes:
He chose the Grand Canyon and the Pacific Ocean + Golden Gate Bridge.
To get there we took Amtrak from Richmond, VA to DC, then switched trains to Chicago. From Chicago we took the Southwest Chief to Flagstaff.
We spent the night at Flagstaff and rented an SUV from Turo to go to the GC the next day. That night we spent at the Thunderbird Inn on the rim of the GC. Due to his age and lack of ability to walk, the rangers at the GC gave us a car pass to drive the bus route so we were able to go along the rim stopping at the overlooks to see. Most handicapped spots are a short walk from the rim. Those that weren’t we skipped. In general, we enjoyed the views - eating take out next to the rim and just marveling at the sites. The following day we headed out along the rim back to Flagstaff stopping at Wupatki National Monument. They have an interesting visitors center telling about the history of the Native People Groups and some ruins that were easy to see without having to walk far. Unfortunately Sunset Crater was closed due to previous forest fires, so we had to skip that.
From Flagstaff we got back on the Southwest Chief (two days after getting off - trains run daily) and made it to LA. Unfortunately, it was too late to make a connection to the Coast Starlight, so we spent a night in LA and cut one short from SF, but in hindsight, an LA stop was a nice break from the train (non-moving bed) so if we were to do it again in the future we’d probably work 2 nights in here and spend the day doing a tour of some sort in LA (plenty to choose from).
Big note here… with the train so late, Amtrak was rerouting people who had booked the Coast Starlight to go up the middle of CA by BUS without telling them that they were going to miss all of the scenic ocean views in CA between the two cities. We refused to accept their offer because we wanted to see the coast - it was a main reason for choosing that route. Because they had an option and we refused it, we had to pay for our lodging in LA and $26 per couple (2 couples) to change the fare. The latter part was annoying, though a trivial cost. What would have been far more annoying would have been being naïve and accepting their offer only to find out there was nothing comparatively scenic along their route.
The train doesn’t actually go to SF, it goes to Emeryville on the other side of the bay, then buses people to SF (private bus). This drops people off in front of a bank late at night… not ideal. Uber and or Lyft from Emeryville cost more, but will take you directly to your hotel. Due to a vehicle getting stuck on the track, we were delayed in Oakland. H checked Uber from there and it was the same cost as Emeryville would have been (maybe less) - hence - we got off at Oakland and got a ride to our hotel. If plotting the trip again, this would be Plan A to save a little bit of time.
In SF we stayed at the Chelsea Inn (loved it), chosen because it’s directly at a Big Red Bus stop. The next day we took the Big Red Bus around town (and over the Golden Gate bridge) stopping at things we wanted to see (Fisherman’s Wharf and more) and getting back on. As you ride around it gives a great history of the city via headphones. Had we had our original two full days here we’d have done a Bay tour too, but one can do whatever they like, of course.
Returning to Emeryville we opted for Uber again. Then we got on the California Zephyr to head back to Chicago through the Rockies - this is the prettiest route Amtrak offers as per many travel sites and it certainly doesn’t disappoint. You travel through mountains and canyons that are stunning (oodles of tunnels along the way - someone said 50ish?, most smaller, but one crossing the Continental Divide is 10 minutes long and was built back in the 20s if I remember correctly), then descend into Denver before nightfall and heading to the plains. From Chicago we retraced our route to DC, then Richmond.
Notes about Amtrak’s distance trains.
Don’t expect them to be on time. Freight trains get the right of way and there’s a lot of freight out there right now. They also have to go slow for heat or rain to avoid making the news. The joy is seeing the sights along the way without having to drive. It’s not a good option for a Type A, “want to get there NOW” person.
Rooms are awesome, but pricy. They have a small private bathroom within them - something FIL needed - but remember that leaves the smell in the room too. The bottom bunk is relatively comfortable. The top bunk is an adventure - you need someone able to get up and down in it. You can see out both sides of the train if you leave your door open, but one side is better than another.
Roomettes are less pricy but don’t have a private bathroom and you can only see out one side of the train - not so good if you’re on the “wall” side of the canyon instead of the river side or similar. There is a terrific observation deck in a car open to all, but it can get full and some conductors will limit people’s time there during the prettiest part of the ride. The bottom bunk isn’t as wide as it is in the rooms. The top bunk is pretty similar in both. In rooms you sleep with your body across the tracks. In roomettes you sleep with your body the same direction the train is traveling. Sleeping on the train takes a little getting used to. Some folks hate it. Some love it. It can depend on who’s driving. We had one really rough night when I’m sure they were trying to make up time, but it was bumpy!
Both rooms and roomettes come with meals and drinks included, that includes one alcoholic drink with supper. You can eat in the dining car or your room/roomette as you prefer.
We spent the bulk of our time in the Observation cars on both of our trips. Fellow travelers vary for better or worse. We met some awesome people from all over the planet (literally) and we have less than positive memories of a couple of Boy Scout troops whose chaperones stayed in their rooms and the teen boys acted like stereotypical nasty teen boys (language content, volume, and getting worse when a passenger asked them to remember they were in public). Most people are great.
Scenery-wise you’ll see the bulk of the US from lush forested east coast often traveling along rivers, to plains where the ground looks endless, to mountains, both desert and forested. Wild critters we saw included antelope, deer, elk, wild horses, bison, Bald Eagles, and hares. On the Zephyr you follow the Colorado river a lot, except on the train it’s called Moon River. Plenty of locals like mooning the train from rafts. Don’t look if you don’t want to see it. Most chuckle. I got some neat pics. You’ll also see a lot of farming of various types - and homeless towns in cities. In several places people will be taking pictures or videos of the train - or just waving as it goes by.
H and I enjoy train travel. FIL loved it. All three of us just love watching the scenery go by and we can roll with the time schedules as needed. I took my Aunt along and she wasn’t as impressed, but liked seeing the GC and mountains, etc. It was more difficult for her to adjust to the way things are on a train (hence, my Type A warning).
Not all trains have rooms/roomettes, but where they do it’s nice if you can afford them. You can’t pick your side though - that’s all luck of the draw. Even if you thought you wanted even or odd numbers, you don’t know which direction the car is going to be put on the track. Cars vary - even on the same train. Coach passengers can pay for food in a cafe car. It’s pricy and not exactly healthy fare, but it was tasty (hot dogs, pizza, etc).
People around me have asked for cost… so I’ve gotten used to giving it out. We had a room for H and FIL and a roomette for my aunt and I on the Southwest Chief (both sections), and the CA Zephyr. My aunt came from Syracuse, so she had her own roomette returning from Chicago - coach getting there due to running out of roomettes. I had my own roomette from DC to Chicago and back. We were coach on the Coast Starlight and Richmond to DC and back since we weren’t spending a night on those trains. In all motels we had two rooms - one night in Flagstaff, one on the GC rim, one night in LA, two nights in SF. Then there were various Ubers, the Turo car rental, souvenirs, and eating at the destinations plus on the Starlight. With everything added we spent about 14-15K. It was well worth it to us. YMMV
Feel free to ask any questions if something wasn’t clear.