The real problem is that the size of the House of Representatives has been frozen for 100 years. The number of electoral college votes a state has is equal to the number of reps and senators they have. Since the House hasn't grown alongside our population, the relative representation for rural areas has steadily grown more and more.
Ending the cap on the House would balance out the electoral college issues and help reduce the constant congressional deadlocks we're seeing.
The bigger problem is that the number of seats in the House has been frozen for about a hundred years. Our population exploded, but our number of representatives stayed static, so places with the most people actually get less representation in congress.
On top of this, the number of electors a state has its equal to the number of representatives that state has in the Senate and the House combined. So more populated states also get underrepresented in the presidential election.
The Three-Fifths Compromise was absolutely fucked, but it's not what is deadlocking the House now and its not what is letting a people lose the popular vote and still go on to be president in 21st century elections.