Model‐based systems engineering (MBSE) is advocated as one important means to deal with increasing product complexity. In this paper, we investigate the increasing interest and use of MBSE in the aerospace domain. The growth of MBSE tools causes new challenges in the corresponding tool‐chain development including data and information management, tool's applicability identification, tool‐integration, etc. In this paper, a literature survey into trends and usages of large‐scale MBSE tool‐chains is presented. It is found that the key functionalities include functional roles, elements, abstraction levels and tool integration techniques. Additionally, we propose a methodology to provide guidance in optimizing future MBSE tool‐chain functionalities for the aero‐industry. In closing, we present a case study in order to illustrate the decision making process required to develop expected tool‐chains by the proposed methodology.