hii akshay 

both are colleges are very good where as the VIT is a Private university the fee would be high as well along with that you will  have to take addmission through the VITEE only apart from that both have the same quality of the education is also good in Pune insititue , where as the placement are also good in the both the colleges as well but to be frank on the disadvantages of pune college the infrastructure is quite low and the few teachers are quite rude as well

coming disadvantages of the VIT is Bhopal is newly formed branch the development of the campus would be less comparitively to VIT chennai,Vellore 

rather in my point of view i would suggest the VIT since you will have lot more exposure and the you will be having the mixture of the people in there and the placements would be also good but only reason is fee is high

hope this helps