This thesis presents an effective methodology and tool set, that explicitly considers technological uncertainty, to enable design, development, and assessment of alternative system concept architectures for an autonomous unmanned surface vessel (USV) in a system of systems (SoS) context. Complex system designs often fail due to poor communication of customer needs and inadequate understanding of the overall problem. This frequently results in the design team missing the mark in transforming requirements into a successful conceptual design. Effective system design requires a defined, flexible, and structured context within which new technological ideas can be judged. Alternative physical architectures are then modeled, simulated, and compared to find the \"best\" solution for further examination. This thesis uses model-based systems engineering (MBSE) principles to develop a multi-criteria decision making (MCDM) model that allows designers to perform a solution neutral investigation of possible alternative physical architecture concepts. This ensures a consistent quantitative evaluation of warfighting capability, suitability, effectiveness, technology maturation, and risk before and during a program execution. This effort is in support of an extended program to design a system of unmanned systems intended to provide the DoD with a coordinated, multi-domain, multi-mission, autonomous security and warfighting asset.