This topic has me wondering how many routes don't take the shortest route between endpoints. Come to think of it, there are at least 8 LD routes that take longer routes than necessary. Below are the ones I can think of along with a faster alternative route.
-California Zephyr (UP across Wyoming)
-Cardinal (LSL Route)
-Coast Starlight (via Central Valley)
-Empire Builder (bypass Grand Forks)
-Silver Meteor (FEC)
-Silver Star (FEC, A-Line through Carolinas)
-Southwest Chief (Southern Transcon via Texas Panhandle)
-Texas Eagle (via KC and OKC)
I'll try and answer this one.
-California Zephyr: Mainly because the EX Rio Grande is considered by the general public to be one of the most scenic railway journeys in the United States. The Burlington Route, Rio Grande, and Western Pacific really out did themselves when it came to putting this train together, it was a train designed around scenery and not speed unlike the overland route. The CZ even in the streamliner era out performed on ridership over the Overland route, scenery sells.
-Cardinal: This is due to West Virginia needing service, especially when they had a powerful senator who preserved this train. Originally the gateway for the C&O Route across the West Virginia was Cincinnati, OH and Amtrak didn't want to have an additional hub there. Which in retrospect is a really dumb move on their part because Cincinnati is home to a ton of high potential corridors CIN-CLE, CIN-DET, CIN-CHI, CIN-PGH, and CIN-STL.
-Coast Starlight: Again scenery sells the Coast Daylight the predecessor had a fantastic track record on this route. At one point it was the most profitable train in the country.
-Empire Builder: There is a more direct route between Minot and Fargo and historically that was the route of the Empire Builder while the Western Star went to Grand Forks. The line to Grand Forks I believe has less traffic which makes it more appealing. I actually don't have a good answer on this one.
-Florida East Coast: One great reason to bypass this route Walt Disney World. Such a great traffic driver for the Florida Trains. The Seaboard and Atlantic Coastline worked hard to turn Florida into an all season destination in the 1940s and 50s, and Disney delivered that in the 1970s. A large ridership generator.
-Silver Star in the Carolinas: Mostly because Columbia and Raleigh deserve to have service as state capitols, and they both historically had great service between Florida and New York on that route. Had the Norlina Sub not been ripped up in North Carolina the route would be substantially shorter than it is today. One day they claim they will reopen it, I will believe it when I see it.
-Southwest Chief: Part of the reason they don't take the Southern Transcon is because that is a super busy stretch of railroad. That and it doesn't have that many population centers along it's route aside from Amarillo. The current route has Albuquerque and in Santa Fe days had a train connection to Denver from LAJ. The route via Raton Pass has always been the passenger route historically, and it will likely remain that.
-Texas Eagle: This train really isn't that indirect in my opinion. Of course the original Texas Eagle actually split into sections to service San Antonio, Houston, and El Paso when the Missouri Pacific ran it. This train also serves a unique political motive as well because it adds Arkansas into the network.