Since the FTA and the federal government are always looking at ways to judge projects based on how they fit into a national strategy, it might be good to think about funding transit in this way. Not because we want to be forced into the frame of the FTA, but rather it might get more interest and importance if it ties into a national strategy. Much like the 1950 federal defense highway system, this could be the national defense transit network.
The idea is that if you hop on a plane and go to Columbus, you can get to the major destinations within Columbus and then hop on a train to Pittsburgh or Cleveland and get around in those places without a car. It seems to me that if you made it easy for people from outside of the city to operate without a car, it would make it easier to operate inside of the city.
There are two components, good metro networks and good city high/moderate speed networks. The larger network should connect cities together that are larger but probably don't get as good of airplane service and major cities that generate a lot of short flight trips. The smaller networks should connect, as said before, the major destinations in a region. For example, Denver's transit network is connecting the Federal Center, the Tech Center, Downtown, and Boulder together with transit. To me, making all of these connections should make it easier for creating transit villages where people can walk or bike for many of their trips and make intercity travel easier as well.