This mainly depends on the student and where he or she is from. As the location is the major factor. Both the colleges are more or less the same, choose the one that fulfills your requirements.

• Bhopal might not be a very fancy place like Chandigarh. But this shouldn't influence your choice.
• IISER Mohali is known for its biology department while IISER Bhopal has an extremely good chemistry department. 
• Their labs are well maintained and have every facility required by the students.
• Hostel rooms at IISER Bhopal are a bit small as it was built for one person per room but later the intake became 2 students per room.
• Hostels are Co-ed in IISER Mohali with bigger rooms and balconies. IISER Bhopal has separate hostels for boys and girls.
• There are around 16 clubs in IISER Mohali, fewer than IISER Bhopal.

Both the colleges are more or less similar when considering academics and infrastructure. Therefore choosing any of them will be good for your career.

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.