The difference is in the intent. The British did not settle in India - they built it as a colony and thus, every institution was set up to extract wealth and send it back to the home country. The Mughals, for all their faults, came as settlers. The institutions they set up were not meant to merely exploit and send resources back to another country; the wealth stayed right there, locally.
The fact that there are so few Indians/Pakistanis of English lineage despite 200 years of rule should tell you the intent of the British rule - the land and its people were merely seen as places to exploit, not as places to settle. They were essentially tourists.