You see, that's where I think Amtrak has no business doing business. Let TxDOT design, build and operate an intrastate system - especially commuters. Leave Amtrak to LD work.
Amtrak is interested in providing this kind of service, since it enhances the national system by prodiving feed-in trains. If Amtrak is going to operate the trains, they need to be involved in the design of the routes and be involved in every aspect of the whole scope of work.
This is how I see it, Amtrak's top priority should be the LD trains and the NEC. Those two meet the objective of providing national inter-city service, everything else tends to serve primarily one state. Everything else should not be included in the national system, the other trains should be paid for entirely by the state and local governments in which they operate.
The equipment should be purchased by the states or in the least be leased from Amtrak. All of these state services should carry the distinction that they are not Amtrak trains but trains that Amtrak operates by a contractual agreement. Under the agreement Amtrak would be responsible for every aspect of day-to-day operation of these trains with the distinction that Amtrak is not going to take a financial hit from these services. The contract should be based solely on Amtrak's cost and include a profit to Amtrak for performing this service to the states. All of the fares from these trains should go to the states, and the fares should help cover the cost of the contract with Amtrak. Under this agreement Amtrak would be guaranteed a profit for operating the services no matter how poorly they perform. By separating these trains from Amtrak's main line of business Amtrak would no longer be using locomotives and cars from its national pool to operate these trains, this would free up equipment and protect Amtrak from being unable to fully account for all of the costs involved in the state run services. If nothing else this system would give Amtrak a guaranteed to be profitable line of business.
I do believe if Amtrak wisely invested money into the LD trains and did a better job of keeping up with the costs of each individual train instead of lumping costs together, we would see the majority of the LD trains turn a profit. The NEC in its current state can't be profitable, the NEC infrastructure is worn out, outdated, and too expensive to maintain in its current state. Until the NEC is essentially rebuilt to replace all of the original 1930's era infrastructure it will never be profitable. If the NEC was turned into the modern state-of-the-art system it should be, it would most likely gush cash and make Amtrak profitable and capable of sustaining itself. Also another weakness of the NEC is inaccuracy in charging the 3rd party users of the corridor, usually these inaccuracies do not favor Amtrak and results in Amtrak covering more costs of the NEC than it should be responsible for.