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.

IISERs get generous funding as they come directly under the MHRD of the central Government. Both IISER Bhopal and IISER Pune have state-of-the-art infrastructure and facilities. 

• The labs, lecture halls, academic buildings, hostels, etc. are present at both the institutes. 
• IISER Bhopal has the largest campus among all IISERs. 
• It also has one of the finest sports facilities available in a science institute, both indoor and outdoor. These include football, tennis, basketball, badminton, chess, table tennis, etc. 
• Community centers and Visitor’ hostels are also available.
• The whole campus is wifi enabled.
• It is a self-sufficient campus with facilities like a shopping centre, health centre, bank, etc. all present on the campus itself. 

Therefore, it is not appropriate to compare the IISERs as they all have their unique features.

This completely depends on your choice and preferences. The only thing you should take into account is how the course will benefit your career ahead.

• IIEST Shibpur and IISER Bhopal offer different career paths. 
• IIEST Shibpur is an engineering college and will push you most probably into a technical or corporate line. 
• IISER has a completely different approach. It focuses on scientific research and you will most probably end up in academia or research-oriented jobs.
• IIEST is a very old and reputed institute in the country and definitely, its placements will be better compared to IISER Bhopal.

This decision entirely depends on you. Choose which career path you want to avail yourself and work toward establishing it.