To answer one of your questions, there is not enough business from Orlando to Mobile to run a train. If there were still casinos in Gulfport/Biloxe, then yes that route would make sense. Right now, it would be an empty train and Amtrak cannot afford that.
If you compare the revenue from the NEC to the LDTs, you will see why so much emphasis is put on the NEC. That is where the money is and that is where the most efforts will be expended.
Reasons for terminating in San Antonio rather than Houston are obvious - no crew base in Houston, no facilities to service the trains, etc. San Antonio also allows for connections between the Texas Eagle and the Sunset.
If you think these decisions are made in a vacumn, you are sadly mistaken. You may have some reason to complain about many of the Amtrak management decisions, but as far as this recent disaster - Katrina/Rita, the decisions have been well thought out and have proven to be the right decisions.
I cannot seem to understand everyone's love of the Sunset. It ranks lowest in overall passenger count - 80,000 for fiscal year 05 - through August and third from the bottom in revenue - $9M - above only the Palmetto and the Cardinal. Granted, it is a true trans-continental train, but only barely, given its horrible on time performance. Decisions to focus on hight passenger count and high revenue trains like the Auto Train and the Empire Builder are the correct ones.