From what I've read about the Skunkworks a large portion of Kelly Johnsons success was attributable to his management style, he was a hard ass taskmaster that somehow also gave his people enough freedom and confidence to do their best work. Since the whole operation was in one building the people building the airplanes and the people designing and engineering them would frequently interact when an issue arose. For a lot of reasons I doubt that duplicating what the Skunkworks was back then would be possible today. I can remember as a little kid seeing that building with the cartoon of a skunk on one side and my dad, who was an enthusiast, telling me about what had been built there and what might be going on at the time. I'm still a bit offended they tore the whole place down, what a waste of history.