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So, they need to decide what hardware best serves their needs. At what levels beyond the standard to implement strong cryptography, and to what degree. Which systems need specific kinds of protection, and what technology is needed to provide secure and useful network connections to their men. The Navy has far different requirements than the Army -- see the Army's use of collaborative mapping systems. It's a great, low level system for sharing data. The Navy, on the other hand, would need such systems to be used at a much higher level; the individual squad leaders on a Naval vessel don't need that intel, but reports and information from other vessels might help a ship captain who needs to patrol. Implimenting such a system for differing useage styles, hardware requirements, and access patterns will nesscitate very different final solutions. And that's just an fairly public one; the Air Force needs systems, backups, procedures, and the like to cover information intrusion into their sensor detection systems, and those will all be different than those used by another branch.
Sure, there's a lot of basic overlap. But the existing data security regulations used in other government branches mean that the basic software and hardware needed to do many things exists and can be reused or modified to spec... and some money will just get wasted anyway.