The article examines the methodological issues of strategic planning and governance. They constitute the critical challenges in the field of constructing national strategies in Russia, i.e., of decision-making with long-term irreversible consequences for the economy and society as a whole. Flawed strategies are determined, above all, by incorrect theoretical backgrounds and approaches to forming strategies and mechanisms for their implementation. Lack of completeness and integrity as well as other shortcomings of the strategies do not allow to achieve strategic objectives. The rapid paces of global scientific and technological development aggravate the problem of competitiveness of the national economy and its units. The speedy introduction of digital technologies creates, on the one hand, some volatility, and on the other hand, the ability to fast technology upgrade in a wide range of economic activities, provided the correct response from the control side. In this regard, basic requirements for a strategy were formulated in the article in the form of several groups of compliance. The first is compliance with the evolution of the controlled object, which is examined as a socio-economic system at different hierarchical levels. The second is compliance with the preferences of main economic agents, as well as reconciling their interests. Thirdly, a strategy should be in compliance with the institutional, socio-cultural and other specificities, the formal and informal rules of stakeholders’ behavior, traditions, norms, etc. In general, the strategy must meet the external and internal conditions and factors of decision-making taking dynamics into account. Fourth, there should be correspondence between subject and object, as well as agreement between strategy tasks and the organizational and economic governance mechanisms. Organizational barriers markedly impede Russia’s advance in the field of emerging technologies. In this regard, the results of DARPA’s comparative analysis with Russian counterparts are presented. As we showed, all types of compliances can be achieved through the application of systematic economic theory. Indeed, it synthesizes the evolutionary, institutional, neoclassical, agent and all other known theories, so it allows to obtain a multidimensional, coherent description of an object studied in a changing environment. Systemic assessment of the capacity of technological development helps to design the image of the future, taking into account significant factors, as well as the preferences of stakeholders. Objectives to create the digital economy create a series of critical obstacles for contemporary Russia. Many of them can be overcome with the help of systemic principles of strategic planning and governance; for this purpose we have developed special models and methods. In particular, a fragment of the scheme for the iterative process of constructing a strategy is presented in the article. In the context of the discussion of modern science and technology trends, we concluded that innovation ecosystems should be established and developed, because they match most closely the requirements of the economy based on knowledge and multiplicative contacts between actors. The importance of a special innovation culture is stressed in the innovation ecosystem diagram presented in the paper. Innovation culture promotes the transfer of knowledge and technology; this culture is formed under the influence of digitalization, conducive to growth of interactivity of the actors. It is the innovation ecosystem concept which implements the systemic approach to establishing and developing a new economic system. Strategies which meet the system requirements encourage the development of the innovation ecosystem at different levels of economic hierarchy. In this regard, further research in this direction appears to be extremely promising.