Developing new wave energy technologies is risky, costly and time-consuming. The large diversity of concepts, components and evaluation criteria creates a vast design space of potentially feasible solutions. This paper aims to introduce a novel methodology for the holistic assessment of wave energy capabilities in various market applications based on sound Systems Engineering methods. The methodology provides a consistent hierarchy of performance metrics relevant to the given system of reference, design activity and development stage under consideration as a means to scrutinise wave energy requirements. Full traceability of system requirements and performance metrics is then facilitated by multi-criteria decision tools and aggregation logic, respectively. The qualitative assessment in the case studies has resulted in very different rankings of System Drivers and Stakeholders for the two market applications considered. However, the Stakeholder Requirements and Functional Requirements present a small variation in the weights for the two application markets which results in a quantitative assessment with very similar Global Merit. Finally, the performance benchmark using the Commercial Attractiveness and Technical Achievability concepts enables a more objective comparison in the utility-scale and remote generation markets and a way to concentrate innovation efforts before proceeding to the next development stage.