During aircraft development, mathematical models are elaborated from our knowledge of fundamental physical laws. Those models are used to gain knowledge in order to make the best decisions at all development stages. Depending on the application, different models can be used to describe, in one way or another, the aircraft behavior. The goal of this paper is to develop a high-fidelity aircraft simulation model that is exceptionally capable, flexible and responsive to the needs of the researchers. The proposed model includes nonlinear aerodynamic coefficients, a generic engine model and a complete autopilot with auto-landing. The simulation model has been designed to help researchers develop and validate new algorithms for trajectory optimization, control design, stability analysis and parameter estimation. To make it easy to use, the simulation model also includes algorithms for stability and control analysis. Methodologies based on Nelder-Mead's optimization algorithm with a friendly user interface have been developed, allowing the trimming and linearizing of an aircraft's model for any flight condition and any configuration. Similarly, the simulation model includes a flight control system (FCS) and a complete autopilot (AP), allowing aircraft to follow a specific trajectory. The FCS and the AP have been designed and tuned using a modified Genetic Algorithm and the Particle Swarm Optimization algorithm. A level D flight simulator of the Cessna Citation X was used to validate the proposed methodology. The results show that the simulation model presented in this paper is accurate and could be further used to analyze the business aircraft Cessna Citation X's behavior. The simulation model could also be adapted for its use on other aircrafts.