I have fairly deep roots in IA - my father's family is from the Cedar Rapids area and I spent two years of my youth living in Des Moines. The stalled growth doesn't seem to be related to industry. IA has maintained significant facilities in food production and distribution, heavy manufacturing (John Deere makes its tractors in Waterloo/Cedar Falls), and even aerospace (Collins, formerly Rockwell, employs almost 10 K in Cedar Rapids). Newton IA lost the Maytag plant, but now hosts wind turbine manufacturing that employs about as many people. Des Moines has long had a good share of insurance firms with major offices.
What I think is missing is that neither Des Moines nor Cedar Rapids became a major transportation hub for Midwestern agribusiness. Those roles fell to Chicago, Minneapolis, Kansas City, and Omaha. It seems that a junction between railroads and a major river or Great Lake was necessary. Davenport and the Quad Cities might have fit the bill, but historically the main rail lines crossed the Mississippi north of the Quad Cities at Clinton or to the south at Burlington. Even today the Amtrak stop for Des Moines is in Osceola, 40 miles to the south.
This map suggests that Davenport-Rock Island was sort of a mini-hub for Iowa, but the CRIP never reached the Pacific, even though the bridge between Rock Island and Davenport was the first over the Mississippi.
https://tile.loc.gov/image-services/iiif/service:gmd:gmd415:g4151:g4151p:rr002190/full/pct:12.5/0/default.jpg
Amtrak likely selected the BNSF (CBQ) route across Iowa since they want the train to go through the Rockies (the westbound train leaves Denver in the AM so it is daylight). If efficiency were an issue, I'd take the UP route and make the Des Moines stop in Ames.
Incidentally, I-80 from Chicago to San Francisco is 20 hours faster (30h45m vs 51h05m) and about 10% shorter (2127 mi v. 2440 mil) than the train.
When a hyperloop is built from San Francisco to New York, would it use a great-circle route at 0 elevation? It happens that Chicago is quite close to the SF-NYC great circle, so it could be connected by a vertical shaft of around 600 feet.
Before Amtrak there were competing routes between Chicago and San Francisco. The northern route through IA or the CNW later the Milwaukee Road connected to the UP at Omaha (the UP only acquired the track to Chicago in 1995) and used the Overland Route through Cheyenne similar to that of I-80 connecting finally to the SP at Ogden. The southern route through IA was operated by the CB&Q to Denver connecting to the D&RGW, and finally via the WP past Salt Lake City. There was a third Chicago to San Francisco passenger route on the AT&SF that went south through New Mexico, but didn't include IA.
Amtrak only kept one of those three after it was created. I suspect that the California Zephyr was picked because of the value of passengers going to and from Denver over any city on the other routes. I had the pleasure of taking the Cal Zephyr in 2018 between Naperville IL and Glenwood Springs CA. It may be a longer route, but the scenery west of Denver was spectacular, and better than anything I could see on I-80.
