This chapter considers the existence of conceptual collision when the mainstream of economic theory takes no notice of Schumpeter’s theory of economic development as the systematic doctrine. This raises serious theoretical and practical problems because the innovation development has become a key priority of successful economic policy. This chapter reveals the conceptual nature phenomenon of innovations as central category of Schumpeter’s theory, which is positioned as independent factor creating new added value. Category of innovation may become like a stem cell of the new Political Economy of innovation development. It is shown that methodological underestimation of innovation as fundamental category of economic theory led to the inadmissible gap between the neoclassical mainstream theories and the real innovation processes of modern economic life.