I foresee a time when the NEC is no longer King (boy, will that be a day of serious denial!) and is relegated to "just another route" status.
I don't think this is possible. The NEC will always have a disproportionately enormous section of the population and economy in a staggeringly small area.
I too support a National System, as Amtrak was originally created for.
That said.....if the worst case happens, and Amtrak is eliminated, the long distance trains will be gone, but the NEC will live on in some way or another....perhaps a consortium owned jointly by the various commuter agencies that now operate on different portions of it. They would still run their own portion, but share in a new authority running thru trains over the entire corridor.. Caltrans would probably do similar, and perhaps Chicago's RTA might take over some routes there. Also New York State on the Empire Corridor, and perhaps a few others. Long distance trains might survive as excursion's like the one between Vancouver and Calgary in Canada...
Anyway, let's hope we never get to that point, and we put our regional biases aside, and work together to save Amtrak as it is.....to quote a tag line used by the PRR back in it's hayday...."Serving the Nation".......