Should I prefer IISER Pune over IIT Madras, Kanpur, or Kharagpur for a BS and an MS in Physics?

Yes, you can prefer IISER Pune over IITs like Madras, Kanpur, or Kharagpur. Although this choice is not that significant. If you are interested in research, your bachelor’s and master’s degree are just baby steps. The difference between IISERs and IITs is the student crowd. Since IISER is more research-oriented, you will get to meet people who are genuinely interested in research. Before choosing any of these institutes, it’s better if you talk to the current students and get to know the faculty and facilities of these institutes.