For a good discussion, you almost have to always exclude the Auto Train from the rest of the system. It's it's own unique breed and has a very different business model than anything else in the system.
So - of the three other routes - Houston - San Antonio, El Paso to Alpine, and Savannah to Jacksonville...
Alpine to El Paso is 3hr:16m, 218 Miles, about 67 MPH. The return is much more drastic, with FIVE hours and 20 minutes allocated. That's an average speed of 40MPH. 200 miles is an awful long distance to go 40 mph...
Houston to San Antonio is 210 Miles. Eastbound takes 4hr 45m going 44 mph vs Westbound a@ 5hr 10m going 40 mph.
The Star of Long Distance, though is the Silver Star. It makes the 148 mile trip in 2:21 going South at an average of 63 mph and North 2:26 going 61 mph. Frankly, I think that the Star should stop at Jessup and that the Meteor should skip it. So the times would be a bit less desireable for those folks in Jessup (wah!) but it would really help make the Meteor the true "Express" train. And when they open up the FEC along the Coast, the Meteor should go down it instead of through Orlando (may make more people unhappy. OK - Extend the Palmetto through the FEC).
Note that the Empire Builder between Spokane and Ephrata WA ties with the JAX/SAV distance of 148 miles. It takes 30 more minutes to travel, too.
California Zephyr has a 177 mile run between McCook, NE and Fort Morgan, CO. It's takes 2:22 minutes, but the increased mileage bumps it to 75 MPH average. That's almost highballing it the whole way! That's the "real" express of the LD world. A TRUE alternative to driving.
I Think I have a winner! California Zephyr between Salt Lake City and Elko, NV is 263 miles of nothingness. It takes 5 hours to sojourn.