Intelligence is a mess, tugged in different directions by DNI, DoD, DHS, CIA, etc. and the core discipline of rationally analyzing information gets corroded by the various mission cultures of other organizations with whom existing intel agencies are affiliated.
1. Simply abolish DHS. It is wasteful, redundant, and ill-conceived.
2. Replace Clapper and transform DNI into a cabinet-level Secretary overseeing the Department of Intelligence and Information, SECI2, serving both military and civilian partners. (Many intel agencies already have this dual function, so it's not much of a stretch.)
3. Reorganize intel agencies (and select research agencies) into discipline-based branches. For example, consolidate all GEOINT analytical and technical personnel in a GI Branch of DII, and eliminate all redundant support personnel. Instant budget savings. Other potential branches would be HUMINT (primarily CIA legacy), Medical & Biological (CDC and others), Economic, Cultural, etc.
The concentration of analytical types altogether in one Department will create a culture that would drastically improve the quality of our intelligence, both for defense and civilian purposes.
4. Having dissolved NGA, use their gigantic new HQ (the third largest federal building in the US, for some reason) in Virginia as the seat for SECI2 and his/her branch Under Secretaries.
5. The National Research Council has already suggested focusing on raw cognitive ability in personnel decisions related to intel analysis, rather than the traditional credentialing and experience criteria. This same standard should be applied to the support, admin, and management of DII, to foster a culture that values accurate, honest, rational intelligence analysis, and to weed out cognitive issues that lead to ineffectiveness and inefficiency. The current generation of IC personnel in these non-analytical positions (who tend to have a Defense culture background) should be transitioned to non-intel civilian DoD jobs or simply let go to save money.
6. For military analysts, DoD should partner with DII, DoD being responsible for combat training and other, basic personnel issues, but DII managing all intel-related education and standards.
7. Rather than dividing missions into military/defense vs. civilian (which would maintain agonistic cultural and political biases that have nothing to do with rational analysis) missions should be defined as long-term research vs. crisis operations, both combat support and disaster relief falling into the latter category.