This paper introduces a conceptual framework motivated by the growing need for a systematic methodology to accurately identify requirements and improve the design of cyber-physical systems (CPS). The proposed approach focuses on addressing the needs of users and stakeholders by presenting an ontology-based requirements engineering methodology that integrates a comprehensive security, privacy, and safety threat model. This model is adaptable to any CPS design, particularly in the context of intelligent transportation systems and cyber-physical infrastructure. The methodology emphasizes a user-centered, system-oriented approach from the outset, leveraging the “X-by-design” principle, ensuring that critical requirements like security, privacy, and safety are embedded throughout the design process, rather than being addressed retroactively. As a case study, the paper demonstrates how this model is applied in a research project focused on the use of connected and autonomous electrical vehicles (CAEVs) in smart transportation and mobility systems. This approach offers a holistic solution to CPS design challenges by considering all key requirements from the very beginning.