Modern aircraft can be seen as heterogeneous systems, containing multiple embedded subsystems which are in today’s simulations split into different domain-specific models based on different modelling methods and tools. This paper addresses typical workflow-driven model integration problems with respect to model fidelity, accuracy in combination with the selected abstraction methods and the target system characteristics. A short overview of integration strategies with the help of co-simulation frameworks including an analysis of the inherent problems that emerge because of different domain-specific modelling methods is being given. It is shown that huge benefits can be reached with the help of a smart system break-up. In detail, the discrepancy between the cyber-physical system simulations and human-machine interaction (HMI) models are being analysed. Therefore, a close look at the typical shortcomings of behavioural models is being discussed, too. To enable an effort-less human-in-the-loop integration into a cyber-physical system simulation, the usage of flight simulation software, offering real-time capability and a graphical user interface is suggested. This approach is applied to overcome today’s complexity and shortcomings in human psychological models. An example implementation based on a commercial flight simulator software (X-Plane) together with a high-performance system simulation tool (Hopsan) via UDP communication is presented and analysed.