The design of a flywheel system for energy storage is herein performed through the Model Based Systems Engineering (MBSE) as an example of mechatronic product development and innovation. Some relevant advantages of the MBSE applied to a material mechatronic system, in some activities, as the requirement analysis, the identification of system capabilities, the definition of architecture and the system validation are identified. Moreover, the paper is aimed at investigating some critical issues arising when the MBSE tools are applied to machine design, being still a domain poorly inclined to exploit this holistic approach. That trend might be related to technical difficulties in assessing an interoperable framework of simulators aimed at dealing simultaneously with functional and physical models. In addition the technology scouting looks poorly connected within the standard SysML diagrams, without introducing some additional charts. A demonstration of the fruitful impact of the MBSE on the machine design is herein proposed, to show some advantages provided as a mechatronic integrated system is conceived and how a complete trade-off analysis could be supported by the MBSE modeling activity.