Naval Ports would be the exception and rely on contractor security or Coast Guard and a Marine Det for security vs entire units.
Aside from that maintain individual states national guard sites and USAF Fighter units for Air defense of the CONUS in this post 9-11 era should remain dispersed to selected individual states Air National Guard bases.
No complete answers ....just ideas as to possible solutions.
Army and AF, okay. Navy and Marines, okay. Army and Marines, sharing a base? BIG problems.