My brother was in a similar dilemma when he got CS in Manipal as well as IIIT Delhi. After consulting a few friends at Manipal, he decided to go for IIIT Delhi. He stated the following reasons for choosing IIIT Delhi over MIT Manipal.
If you want laid-back academics with a vibrant campus life, your choice should be Manipal whereas if you want a rigorous curriculum, then go for IIIT Delhi. It’s just a question of what your priorities are.