The gregreat Compromise wasn't about urban vs rural, it was about large states vs small states. That is an important distinction, no state at the time was largely urban all states were predominantly rural, however some states were larger and had larger populations than other states. Slave states certainly pushed for the 3/5th compromise, knowing it would benefit them under the constitution, in both the house and the electoral college.
Besides a popular vote would have been impossible at the time, the slaves states wouldn't have stood for it and all of the states had diffrent voting laws which would have made the popular vote near impossible to implement.
The electoral college was never intended to operate as it currently does, the electors were not supposed to be pledged, or required by law, to vote for a specific person. What the electoral college does now is destroy democracy by making sure presidents only campaign for a small number of swing states, and only for a small number of voters in those swing states. And the swing states arent the small states either.