Trend of AI application as a tool for research is analyzed. It is based on “Automated Research Agent” model performing the entire research cycle (generating new ideas, writing code, conducting experiment, selecting and visualizing results, writing a full-fledged article according to academic standard). Innovative approaches to AI research capacity application are considered including: 1. conducting a classical experiment; 2. modeling AGI based on technology of superimposing sense-cognitive structures of human and artificial intelligence for identifying strategy of their synergetic co-development; 3. providing hybrid system in which the differences in patterns detected in the generative intelligence subsystem make it possible to find rules that are absent in the symbolic intelligence subsystem; 4. using emergence in the search for patterns inaccessible to human intelligence. Innovative multidisciplinary approach to holistic system research and reasons for its blocking are considered.