Recently one of my cousins graduated from IIIT Bhopal. If you want to examine the above two options then surely I would say IIIT Bhopal is better because of certain problems IIIT Kalyani encountered in the past few months. 

Even after, the major problems which IIIT Bhopal was meeting were Clubs and hostel issues. About two to three clubs of IIIT Bhopal have started playing into the role on their own and in the coming year. You can even expect more, although few clubs of MANIT also have IIIT Bhopal students. 

As I already mentioned before the distance of the Hostel is an issue with the administration which is supposed to be settled in the coming future. Apparently, the classes for the students of IIIT Bhopal are occurring in NTB-MANIT. The lab facilities for IIIT students have been made available.