You should prefer AIIMS Jodhpur. It offers better academics and teaching. The college location is good, it's hardly 2-3 km from the city. AIIMS Jodhpur has a computerized patient management system which makes it easier to conduct research in OPD and IPD settings. Among the new AIIMS, it has the maximum number of PG seats.

Spots facilities of the campus are top notch. There are separate grounds for football and cricket, 2 basketball courts, 2 volleyball courts, 2 hockey grounds, 3 tennis courts, and the indoor games facilities are good as well.

Both AIIMS Jodhpur and Bhopal have similar closing ranks. So, you can choose either of these two institutes based on which is near you. But when compared AIIMS Jodhpur is better than AIIMS Bhopal. 

It has more patient load and it also offers better academics. You can check the PG results. Also, the living condition is better in Jodhpur.