Avionic system developers are currently working on innovative technologies that are required in view of the rapid expansion of global air transport and growing concerns for environmental sustainability of aviation sector. Novel Communication, Navigation and Surveillance (CNS) system designs are being developed in the CNS/Air Traffic Management (CNS/ATM) and Avionics (CNS+A) context for mission-and safety-critical applications. The introduction of dedicated software modules in Next Generation Flight Management Systems (NG-FMS), which are the primary providers of automated navigation and guidance services in manned aircraft and Remotely-Piloted Aircraft Systems (RPAS), has the potential to enable the significant advances brought in by time and trajectory based operations. High-integrity, high-reliability and all-weather services are required in the context of four dimensional Trajectory Based Operations / Intent Based Operations (TBO/IBO). The NG-FMS and the Next Generation Air Traffic Management (NG-ATM) systems are presented and they allow the development of automated negotiation and validation of the aircraft intents in real-time. After describing the key system architectures, the mathematical models for trajectory generation and CNS performance criteria evaluation are presented. In this paper, the navigation performance is evaluated specifically and in a similar manner, communication and surveillance performances can also be evaluated. An evaluation of the proposed concepts and methodologies is accomplished by modeling and simulation activities. The results demonstrate the functional capability of the novel avionic system to generate cost-effective trajectory profiles satisfying both operational and environmental requirements, as well as satisfying the required navigation performance criteria.