http://sebokwiki.org/wiki/FAA_Advanced_Automation_System_%28...
http://articles.latimes.com/1988-08-11/business/fi-288_1_air...
Basically, none of these huge companies want to do this kind of work unless the pay is obscene. And then once it's obscene, the companies all fight over it and throw each other under the bus. Court battles aren't even the half of it. They hire lobbyists, contribute to campaigns, and every 2-8 years there's some amount of government shuffling. So nothing is actually ever very consistent within the government. New politicians, new bureaucrats, new policies, new ideas (they think anyway), and they basically have been scrapping previously done work and starting over multiple times. And it's been longer than 40 years.
Perversely, running on vacuum tubes makes the old system a more security hardened system than what we're likely to end up with. We should hope the NSA has hacked the FAA and ATC as a defensive measure.