RGIPT IDD is a relatively new institute in comparison to IISER Bhopal which is more established. RGIPT IDD has gained popularity because of its quality of education.
Ultimately, the ‘better’ institute for you depends on your own interests and goals. If you are willing to pursue a career in applied fields such as artificial intelligence or machine learning, then RGIPT IDD is great for you but if you want a career in research or academia, then IISER Bhopal may be a better choice.