Multi-Int Fusion Systems are complex due to the need to architect a solution that covers a broad domain space with diverse functional requirements. Consequently, some of these requirements can seem orthogonal, such as the need for real-time embedded processing for on-board platforms juxtaposed with large-scale enterprise systems comprising application servers, database farms, and service-oriented architectures. Add to these considerations, the need to address Information Assurance, which includes functionality for confidentiality, integrity, availability, authentication, and non-repudiation - all applied to a broad set of heterogeneous data and implemented across multiple organizations spanning transnational jurisdictions. These challenges render the traditional systems engineering approach ineffective. This paper explores key issues innate to Net-Centric Multi-Int Fusion Systems, and offers SoSE principles for a top-down analysis of functional requirements and guidelines for reconciling design trade-offs - essential steps to ensure the synthesis of a holistic and robust SoS architecture.