The article presents the results of the influence of the scale of universities on their contribution to the goals of the national project «Science and Universities» and their positioning within the framework of the «Priority 2030» Program. The study of a number of indicators has recorded that, within the framework of the current assessment system, universities of a smaller scale have an advantage, which creates a risk of mismatch of tasks. The authors propose a change in the methodological approach and a comprehensive assessment methodology, taking into account both the tasks of the national project and the efficiency of universities.