Hey,  

I guess there are not much disadvantages in that except extc is not much known course,  so very less companies prefer students of this course but many companies do visit there.And the disadvantage of choosing CSE at SPIT is that the fees is higher than VJTI .Also,  the academic schedule is exhausting,  so you will not get time for preparation for any thing else.

Hope you got your doubts cleared in both the ways!