What should I choose between IIT, Kanpur (materials science and engineering) and IIT, Kharagpur (metallurgy and materials science) for M.Tech and why?

Both IIT Kanpur Material Science and Engineering and IIT KGP Metallurgy are excellent programs. To choose one of these, you first determine where your interests lie. done 

• If you are inclined towards the field of materials science, then choosing IIT Kanpur will be beneficial for you. In fact, it has many faculties that are globally known for their achievements and contributions in the field of electronic materials, biomaterials, optical materials, ceramics, metallic glasses, and corrosion.
• On the other hand, IIT KGP Metallurgy is a viable option for those interested in areas like physical metallurgy, powder metallurgy, characterization techniques, and material testing. The location of the Institute is excellent for metallurgy eight Tata Steel and National Metallurgical Laboratory are both in close proximity to the institute. This is good news for research enthusiasts.

Both the institutes and programs are good and thus the final decision should be based on your area of interest considering the fact that IIT Kanpur has a much more rigid culture in terms of academics.