I was also having such types of questions when I was preparing for JEE. One cannot say that all IITs are better than IIITs. IITs are famous from the tag of IIT. You have to go individually targeting a specific branch. IITs are good but see whether the branch you are interested is good there there or not.
We all say that IITs are the best. But it all depends on the candidates who study there whether they work hard to them proud and famous or not? So it all depends on one's hard work.
Recently a boy from MNIT made a record package of 1.34crores from Facebook. Why can't anybody till now made such an achievement from IITs.
If students from some X college are moved to IITS and the students of IITs are moved to X college, then I am sure that the X college is going to gain reputation and the IITs would have a decline in its status.
It all depends on students. Yes, facilities, laboratories etc matters but they cannot stand in front of intelligence and hard work.
But If we make our admissions to IITs then we prove that yes we have within us that intelligence, hard work etc.
As per question I must tell you that in IIIT Hyderabad, computer science is very good. If you are not able to get admission in the top IITs then go for good branches in IIITs.
Always choose your branch of interest and not the top branch of the institution.
How to get into them?
Hard work, intelligence, smartness in your work, right guidance and study material are the only keys to get into such institutions.
Stay away from bad companies, the time you are having today is a golden chance for you.
We always had this thing in our mind, to get free from studies and to enjoy our life.
Here is my personal experience-
I dropped two years one for JEE, taken coaching from Bansal Institute. I was not able to make to the cut off. I scored 157 and cut off was 180. I drop one more year for AIEEE thinking that I would have taken coaching for AIEEE, I would surely had scored a good rank in AIEEE. At that time I was preparing in home.
The whole year I realized that What is my life without education? Without studies? That year made me to know the exact meaning of-'Work is Worship'. So never feel doing hard work as a burden.
I suggest you that even if you are not selected in JEE then go for NITs, the top ones.
And if not got a good rank in AIEEE then take a year break and do the best you can.
Success is a journey not a destination.