It was part of a compromise from the southern states, because they were less populous, and would therefore have much less influence in a national popular vote.
James Madison hated it and argued against it, but wasn't able to affect that change.
I don't think it's a good idea, and I don't think it's necessary. It doesn't even do what it was designed to do, boost the influence of less populous states, but instead creates a huge fight over swing states instead.
Edit: Found an article on it that, after some skimming, partially refutes my point. It wasn't necessarily about lower population in the southern states. It was because they couldn't count their slaves, so the electoral college and the 3/5's compromise put them on equal footing with non-slave states. It always comes back to slavery. Every god damn time :/
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