Much better! Coherent argument. Facts and citations. Good stuff.
But when you say,
I acknowledge that the compromise was necessary to get the southern states to join.
you are flat out wrong to the point of having it all ass-backward. First the Great Compromise was proposed by Roger Sherman of Connecticut after the Virginia plans and New Jersey plans for legislative representation both failed. Guess which one was based on population? Yes it was the plan put forth by Virginia, a slave state. It had the largest population of all the colonies, New Jersey, a free state, wanted each state to have the same number of representatives. The Grest Compromise was necessary to get the small states to join especially the small free states. The free states still felt it was unfair because the slave states had a lot of slaves who would get counted in the census and they feared that would give the slave states too much control. So the free states were the ones that were placated by the overtly racist 3/5 compromise. They were also able to get a date certain to end importation of slaves. Part of that was motivated again by the fear free states had of the representation based on population when the other side was more populous to begin with and could potentially import a huge number of additional slaves. Your basic misunderstanding seems to be that you are imposing the conditions of 1860 back on the world of 1787.
I have taken no position on the merits of popular vote election of the President. My opposition is to use of a sly trick to evade the need to pass a Constitutional Amendment to effectuate such a basic change. A change negating the Great Compromise that is fundamental to the Constitution needs to be done legitimately by amendment. Anything less carries an unacceptable risk of chaos. You are sure confident you can tinker with the key parts of a system that has survived 230 years and it will all work out fine. What hubris.