Both IMC Manipal as well as Mangalore have their own unique strengths and weaknesses. In terms of academics, both colleges are almost similar with some of the most experienced teachers, and excellent clinical exposure. The only major difference you will see is that KMC Mangalore has a dispersed campus so you have to travel through a city while you study. Mangalore therefore offers a more flexible life and offers an environment that helps you become a more independent person.
I would recommend Kasturba Medical College even over Government Institutes for MBBS training.