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One of the biggest problems, as the NRC sees it, is actually that politicians don't seem to understand the technical aspects of these kinds of large projects. They praise the FAA in the introduction, finding that, "An important part of NextGen is addressing the need to replace aging equipment. Such modernization is essential and important. Replacing or upgrading systems while continuously and safely operating the whole system is an intricate undertaking, a process that the FAA seems to have mastered. The successful operation of such systems requires ongoing alterations and improvements, not just the occasional repair of faulty equipment and software." (National Research Council, 1) The FAA can't just shut down all airspace for a month in order to hit a reset button. All new systems have to be built taking into account the many different existing systems in place, the limitations of those systems, and in order to ensure a safe transition. Implementation has to be phased in and delicately built up.
That said, there are clearly some deficiencies at the FAA. The key trend that the report seems to get into is that while FAA is effective in risk management and systems architecture understanding, they tend to have a very near-sighted approach to problems, usually seeing new systems as being layered onto existing, a decidedly cautious approach. If anything, the FAA is doing its job while Congress seems not to be, "As for any large-scale government IT effort, a long-term commitment is important. ...there is a specific need for support of ongoing maintenance and modernization (upgrades) and refreshing and modernizing of both hardware and software to provide reliable, cost-effective operation. Too often in government, funds are allocated for specific (new) programs or projects without sufficient
allocation for the full life-cycle costs and for maintenance and refresh of existing (and still important)programs." (53). Basically, Congress has created a situation where funding for the FAA's normal capital and operating needs are tight, but anything with "NextGen" in the name gets a ton of money (comparatively). In such an environment, the FAA has quite a lot of incentive to basically use NextGen in order to support its ongoing capital and operational needs in terms of regular hardware and software upgrades and maintenance. The solution here is obviously that there needs to be a better understanding in Congress that large projects like NextGen require a careful, managed approach with expectations tempered by technical realities, that the FAA has not done a great job communicating those realities does not mean they don't exist. The view that we can just "fund the new program" and then everything will magically be fixed because systems are easy to put in place is highly problematic, and it's definitely a problem in Congress, but the NRC report is saying not so much at the FAA.
TLDR version: NRC Report isn't "scathing", the real problem is that Congress' expectations don't take technical realities into account at all, while the FAA doesn't have the staff or technical leadership capabilities to develop transformational systems, so they use their technical expertise to instead implement modernization.
Cited:
National Academies Press, "A Review of the Next Generation Air Transportation System:
Implications and Importance of System Architecture (2015)" http://www.nap.edu/download.php?record_id=21721#. Online PDF, Accessed May 4, 2015.