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As System of Systems challenges become more pronounced, we are especially interested in a) the notion that each particular SoS problem is unique, possessing different sets of traits to differing degrees a) in the midst of this diversity, developing appropriate modeling for purposes of decision-making support. Because individual systems can operate independently within an system of systems, many traditional engineering methods and tools used to design large-scale, but monolithic, systems do not appear to work for designing systems of systems. A taxonomy and common lexicon are employed in putting design problem formulation and modeling on a sound footing. This paper highlights the most recent version of the taxonomy and its use in guiding research to shape the modeling approach for three distinct transportation-related application case studies.