Both IISER Pune and IISER Mohali offer good academics and placement opportunities to students. In terms of facilities, both institutes are on an equal footing now. The research output of IISER Mohali is catching up. In terms of coursework, electives at both institutes are slightly different. You can check out the course structure and faculty profile from the official websites. Before joining, you should also get to know about the culture of the places. You can talk to the current students from both institutes. Do your research about both institutes and choose according to your convenience.