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The continuous growth of air traffic demand, skyrocketing fuel price, and increasing concerns on safety and environmental impact of air transportation necessitate the modernization of the air traffic management (ATM) system in the United States. The design of such a large-scale networked system that involves complex interactions among automation and human operators poses new challenges for many engineering fields. This paper investigates several important facets of the future ATM system from a systems-level point of view. In particular, we develop a hierarchical decentralized decision architecture that can design 4-D (space +time) path plans for a large number of flights while satisfying weather and capacity constraints of the overall system. The proposed planning framework respects preferences of individual flights and encourages information sharing among different decision makers in the system, and thus has a great potential to reduce traffic delays and weather risks while maintaining safety standards. The framework is validated through a large-scale simulation based on real traffic data over the entire airspace of the contiguous United States. We envision that the hierarchical decentralization approach developed in this paper would also provide useful insights into the design of decision and information hierarchies for other large-scale infrastructure systems.