There is a myth that all Indian Muslims wanted Pakistan. Facts are otherwise. No wonder there are almost equal number of Muslims who decided to live back in India. Here is letter from Indian Muslims to UN;
I am a Mohajir in the purest sense of the word: my mother was born in Ranchi (present day Jharkhand), my father in Patna; my maternal and paternal side were both from Bihar. My grandparents (maternal and paternal) both left along with my parents (who were very young) in 1947, along with some relatives from both sides. There was a lot of family left behind too, namely the siblings of my maternal grandparents as well as most of my maternal side. My maternal grandmother told me recently that she couldn't talk to her sister on the phone after 1947, and she couldn't be in touch with her for a few years. It's my understanding that most Muslims DID want to come, but many belonged to the impoverished states UP and Bihar. Getting to Pakistan was a huge distance, and they couldn't afford it, plus there was also this danger of getting killed on the way via land. My grandparents and my parents took a train for Bombay (because Maharashtra had no direct border with any part of Pakistan, so it was relatively peaceful), and then went to Karachi by ship. They could afford it, other poor people from Bihar (which includes many of my relatives) couldn't. So the Muslims left behind didn't stay because of their choice, they stayed because they couldn't afford to go.
Indian Muslims have always been suffering an inferiority complex against Pakistan after 1947. They have had to endure some very tough times after 1947, where they had to prove they were loyal to India and had nothing to do with Pakistan. They felt that the creation of Pakistan would cause them a lot of harm, and they were very apprehensive about how they would be treated in Hindu majority India. If anyone with links to Pakistan right after 1947 was found, they would be in trouble. And in about 50 of the 60 years of the independence of both countries, Pakistan has performed better economically than India, which is another reason for their inferiority complexes. It's only till recently (after 2000) that India has done better than Pakistan, and look at the "happiness" of these Indian Muslims.