Model- and component-based design have yielded dramatic increase in design productivity in several narrowly focused homogeneous domains, such as signal processing, control and aspects of electronic design. However, significant impact on the design and manufacturing of complex cyber-physical systems (CPS) such as vehicles has not yet been achieved. This paper describes challenges of and solution approaches to building a comprehensive design tool suite for complex CPS. The primary driver for the OpenMETA tool chain was to push the boundaries of the “correct-by-construction” principle to decrease significantly the costly design-build-test-redesign cycles in design flows. In the discussions we will focus on the impact of heterogeneity in modeling CPS. This challenge is compounded by the need for rapidly evolving the design flow by changing/updating the selection of modeling languages, analysis and verification tools and synthesis methods. Based on our experience with the development of OpenMETA and with the evaluation of its performance in a complex CPS design challenge we argue that the current vertically integrated, discipline-specific tool chains for CPS design need to be complemented with horizontal integration layers that support model integration, tool integration and design process integration. This paper will examine the OpenMETA technical approach to construct the new integration layers, provides and overview of the technical framework we established for their implementation and summarize our experience with their application.