Hello Pavan,
Well let's just say the difference is the same as that of a certain Virat Kohli and a certain Joginder Sharma.
Both won world cups for India. But joginder sharma's heroics were one time wonder but Kohli is a trademark of consistency.
Similarly MIT Jaipur might claim some accolades from time to time but MIT Manipal is and will remain among the best engineering colleges in the country.
As you know that Manipal campus is relatively older, top rankers choose it. Also the faculty could be better as it is the main branch. There are exceptions though. And placements are also better.
Thank you ,
Best of Luck for your future.Hope it helps you ,feel free to ask any query
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