The purpose of the study is to identify the main problems and prospects of the education system in the context of innovative development, as well as the intellectualism of future teachers. The authors of the article conducted a factor analysis of the ongoing reforms in the education system. The transition of the economy to the innovative way of development and the overall socio-economic situation in Kazakhstan and other countries requires a rethinking of some priorities prevailing in politics and focusing on building a new type of society based on the development and mutual integration of three main elements such as education, innovation, and research. These elements are impossible without intellectualism and critical thinking. The formation of innovation policy should contribute to the development of a set of measures in the system of higher professional pedagogical education that organize and stimulate innovative activities and promote the integration of education in the scientific and technical space. This integration process will serve as the basis for the formation of the strategy and tactics of innovative development based on intellectualism and critical thinking.