Beneath many of America's largest cities is a subway system, an underground train that takes people places at high speed. Most of them were built to relieve surface traffic, which in large cities quickly grows to unbearable levels. Unfortunately, they also tend to be extremely expensive, mostly because the city waited until traffic was unbearable to install them, at which point the land was crowded, difficult to work with, and expensive.
I think we should install a high speed national subway system that can quickly haul people between large cities, with further nodes installed in likely to grow areas. The advantages of this are numerous: people can be evacuated in case of a disaster, troops can be moved in a literally undetectable way, and subways use far less energy than planes or above-ground trains. If we do this now, while much of the country has not yet been developed, we can do it for far less than if we had waited. In addition, the additional stops will lead to the growth of new cities, and with it, high tax bases.
We can also build this in levels, so there would be a deep level that would transport people from city to city, a shallower level that would take people around within cities, so that neither could collide with the other. The deeper one would move at much much higher speed, taking people anywhere in the country within hours. Possibly even to Hawaii and Alaska, although I predict these hubs will be the last ones built because undersea tunnels are mind-bogglingly expensive.
For safety, engineers should consider possibilities of security issues, such as biological or gas attack.