I read "Skunk Works" recently. For those who don't remember, it was a unit of Lockheed Aircraft which developed innovative planes, particularly the U-2, the stealth fighter, and the RB-71. By having good people dedicated to the job led by someone who could navigate the bureaucracy and still inspire, it did damn well.
They were not involved in the F-111 program, known to geezers as McNamara's TFX. It seems from the wikipedia article for it that it turned out okay, but back in the day it was heavily criticized for being over-complicates and too expensive as a result of McNamara's pet idea--have one plane which could serve both the Navy and Air Force.
My initial reaction when reading this Salon piece on the F-35 was to remember the TFX.