FKPcamper, what you have written is purely what you have experienced on a personal level. I have a Pakistani father & an Indian mother (who surrendered her Indian citizenship when she married my Dad in Pakistan), & family in both Pakistan & India. I've been to India a few times as well. I think Pakistani & Indian societies are very similar. This is my assessment of Indian & Pakistani society:
1) India overall is a more liberal country than Pakistan, Pakistan is conservative.
2) Opportunities to excel in all walks of life for minorities are similar in both countries. Contrary to common belief, minorities in Pakistan are involved in all fields of life in Pakistan, & the only thing they can't be is the PM/President of the country, they can be anything else they want to. Their involvement in Pakistani affairs is quiet, but significant.
3) I feel minorities (& their places of worship) in Pakistan are given better protection than the minorities in India, & there is less bias of LEA against minorities in Pakistan. The security problems Muslims in Pakistan have faced are greater than what minorities in Pakistan have faced.
4) In Pakistan, some religious minorities (especially poor people) might want to keep their distance from the majority Muslims. In India, it is similar as well to an extent. There is a better understanding of minorities in India though, than of minorities in Pakistan, partly because minorities in Pakistan like to keep their distance from the majority, & live peacefully. There are poor minority neighborhoods in both Pakistan & India. But in Pakistan, the poor people live in poor neighborhoods, regardless of religion. Minorities never manage to have problems finding housing in Pakistan based on their religions, which even rich minority people in India do, just because of their religion.
5) In India, while there is a general acceptance of diversity, there is also a "secular Indian-ness" that is expected on some levels. The overly religious people in India can sometimes be perceived wrongly in India, & people might not think they are patriotic enough. In Pakistan, such diversity is not accepted (unless you're in Karachi, or Islamabad to a lesser extent), so if minorities want to remain "closed off" from the majority in Pakistan, they are free to do so peacefully. We do not suspect any of our citizens regardless of religion to be a spy or something.