I loved Kelly's memoir; reading his story and how he did what he did makes it seem so simple in the telling; looking at the many billions wasted by companies trying to get close tells you -- not so fast.
I learned in that book that he actually returned money to the government for, I think, the U-2 project -- they made a few extra planes and had money left over. Amazing.
I'd love to read a longitudinal retrospective of failed skunkworks setups and see why participants thought they failed -- I bet it's a diverse list of reasons.
Kelly had a subversive quality to him that is probably almost impossible to institutionalize; I think it's unusual to find that mixed with some nationalist pride -- in that way, I see him as a product of the war, and the postwar boom.
That plus his broad multilateral intelligence -- seeing design and implementation as one thing that one could expect to understand and possibly master -- stood out for me, reading about him.
Anyway, if a leader like Kelly is needed for a skunkworks, that itself may be quite difficult. I'd guess most large companies would take a functioning "almost as good as" Skunkworks any day, if they could tolerate the guy/gal running it.
I've read biographies of both - well worth reading for anyone who wants to read about great Americans.