This kind of confusion arises among other students. My brother was also one of them and most of his seniors recommended IIIT because it is a premier national institute. No matter this is a new institute but soon this institute will take its place. 

The other reason is that IIIT Bhopal’s mentor institute is MANIT Bhopal where the professors are from NIT. But if you are getting a fee waiver in JSS College then you should go for JSS. 

Most importantly, JSS is a private institution and IIIT is a government college so you will benefit in terms of fees.