In 2009 the nation’s air traffic control system came to an abrupt halt. It would be the second time in 15 months that a technical glitch would throw air travel into disarray and leave air travelers stranded for hours (Conkey and Pasztor 2009). Ever since the National Airspace System (NAS) was developed there have been several attempts over the last few decades to modernize this system with “Next Generation” concepts and technologies. These attempts have often ended in failure. Some of these failures stem from problems developing “gap analysis.” As technology has advanced from generation to generation it has become more difficult documenting gap analysis when comparing current system functionality to future capabilities and programs have suffered from cost overruns and schedule delays. The source of these problems has been attributed to failures that usually occur at the interfaces between systems elements, many times between elements thought to be separate. In determining if the Design Structure Matrix (DSM) is an applicable technique for modeling an actual complex systems of systems, this study will assess whether the DSM approach provides a project representation that allows for feedback and cyclic task dependencies. This study will also access whether the previous data results in an improved and more realistic transition strategy. This strategy will improve system development for the complex NAS systems of systems. The study will utilize a survey of system engineering professionals to document their requirements development process and system integration process and how it impacts system development. Data collected during interviews with system engineering professionals and managers will be used to populate the DSM simulation tool. This data will be further analyzed using the clustering technique to more easily identify and examine interfaces between the clusters. A multiple-case study is also proposed to evaluate the viability of applying DSM to an actual complex systems of systems. With the annual expenditures in both the public and the private sector being in excess of several trillion dollars and international program failure rates hovering about 70%, acquisition officials, program managers, and system engineers need to understand the impact of applying improved systems modeling techniques such as DSM on transition and development strategies that will achieve better cost, schedule, and technical performance.