Dude, Have you ever written GATE. Go to IISc and do your MS or PhD over there.I am sure that you will be kicked off.Getting PhD from IISc is the difficult job. Dude doing MS or PhD in above 50 ranked universities is for better than doing in IITs.
I hope you know Mr.Narayanamoorthy(founder of Infosys)has done his M.Tech in IITK. I hope I dont need to tell about him to you.
One thing that you have to have in your mind that if you are good you can shine. There are some MS students in IITs who is doing for better than B.Tech.
You have to come to IITs and see what these B.Tech people are doing.