Well, this all depends upon your choice of preference. 

• If you are going after a brand name then you can choose IIIT Guwahati. Also, it is worth joining IIIT’s of all new ones for their coding culture is on a boom. 
• If you are planning to prepare for MBA, Civil Services, MS abroad then choosing IIIT G is a better choice.
• If you find the IIIT tag more appealing go for it. Yes, infrastructure wise Thapar University gives a quiet edge to many IIITs and NITs. 
• See, you’re comparing different branches, from which I can directly conclude that you’re interested in CSE more. So, keep this factor in mind too while deciding.
• If you are getting IIIT it means you do hold a good rank. That means you are okay with getting into IIITG even with high fees. If you have got a board percentage of 95+ you can get a 100% TF+DF waiver right from 1st semester.
• One of the important factors for choosing an institute is fees, if you are okay with higher course fees, you can definitely opt for Thapar. Infrastructure at Thapar is way better as compared to IIITs and NITs. 

This was an overall review on IIITG and Thapar University. Factor all these in and make a wise decision.