The importance and inherence of innovations in the context of the current technological paradigm cause the necessity to develop approaches and tools for their effective management within individual enterprises at the level of groups of economic entities and sustainable development of regions of their localization as a whole. The formation of such solutions requires an analysis of the problems of innovative development and innovation policy to identify the basic patterns of their changes, and mutual interaction in the temporal, spatial, and sectoral context. The purpose of the study was to analyze the potential spatiotemporal influence of key factors groups on innovation activity effectiveness and its delay in the context of industry-based specifics of specialization of the Russian Federation regions. The authors considered the variants of manifestation of factors on the initially diverse geographical, socio-economic, political, and other conditions groups (regions) of resources and abilities to assess the influence of specified factors on the systems different by the initial parameters. Moreover, the specific feature is the analysis of factors’ impact on the result of implementation in the systems rather than disparate sets of resources and abilities. The authors analyzed possible specific patterns depending on the structure of this system and its initial conditions, which can serve as the basis for changes in the methodology of innovative development management as one of the key directions of modernization of industrial production and sustainable development of territories. The influence of an attributing factor on the result differed both in direction and in the power of influence between regions, which confirmed the need for the differentiated approach to innovative activity management and evaluation of the results of its manifestation. The analysis shows that the patent activity impact on the volume of innovative goods, works, and services varies greatly depending on the structure of their economic activities. The level of innovative activity is manifested strongly and rapidly in multi-sectoral and mid-specialized regions with an average weight of specialization industries of local and national significance, and in three years, multi-sectoral regions appear to be more sustainable. Almost all multi-sectoral regions show a one-time positive influence of losses for innovative activity, and in three years, it is rather negative for most regions.