Both AIIMS Rishikesh and AIIMS Jodhpur are at the same level in terms of the quality of education offered, infrastructure, and research culture. What sets them apart is the college life experience they offer and the students they attract because of their locations. The PG results prove the credibility of both the institutes so choose one based only on your personal preferences.
AIIMS Jodhpur has a slightly better cutoff than AIIMS Rishikesh as most of the toppers are from Rajasthan and end up choosing AIIMS Jodhpur over AIIMS Rishikesh. This shouldn't be seen as a differentiating criterion.
I am inclined towards AIIMS Rishikesh because of 2 core reasons. The newly launched MCG pattern for all its exams that help you prepare for NEET PG and its splendid location in the lap of mother nature. So it is best to stick to your decision and don’t opt for upgradation.