IIIT-Hyderabad indeed has one of the best CSE programs in the country.
However I feel that a college should not only teach, it should also be a platform to grow your personality, by giving you immense exposure to various things.
IITs(especially the old ones) regardless of branch are way ahead of IIIT-H in this respect. The infrastructure, the flexibiity(it has increased even more in these years because of changes in the curriculum), the strong alumni network, the reputation associated with it etc.
If someone is very interested in math(thereotical CS) , CS or electronics research, one should strongly opt for IIIT-H.
But if your goal is to get a job after 4 years, you should note that you'll surely land up in a great company after 4 years through IIIT-H, but in the long term it might not be very beneficial unless you go for managerial posts, or venture into entrepreneurship(here IITs have the leading edge). Things like these involve handling people and not technologies. The environment at old IITs surely helps in this regard. Companies like facebook even have age restrictions for technical posts.
Many people criticize the path of doing an MBA after an engineering degree. I don't find the path wrong at all. If you want to work in the industry you surely need to learn to handle people. Here your technical knowledge will be a plus point for you. Those MBAs who do not have a technical background don't fit well in the technical industry.
People who take CSE in any college they can get, just because of the fresher packages it rewards are not looking from the long term perspective. Technology changes faster than they can imagine. To keep up with it with increasing age is a tough job!