My answer is specifically for the UG students. In my opinion, JIPMER Pondicherry is a better option than AIMS Jodhpur. It's one of the oldest Indian medical colleges. Let's go through a few pros and cons of the institute to explain further why this will prove to be a better option for you.
Pros
Cons
Any smart person can point out that the pros clearly overshadow the cons and thus we can say that while AIIMS Jodhpur is fast growing, it will take some time to match the level of top medical colleges like JIPMER, PGI, and AIIMS Delhi.