On "that's not the Electoral College, those were just uncompetitive states", they're only "safe" and ignorable because of winner-take-all, which you already agreed is the problem. Under a popular vote there's no safe state to write off: a vote in California counts the same as a vote in Ohio, so no one's surplus can be ignored. The Electoral College is the very thing that makes votes in 38 states worthless.
And it only gives "the less populated a voice" in the dozen swing states. Rural voters in California, upstate New York, and rural Texas get nothing today. So it doesn't protect rural voters, it protects rural voters who happen to live in a swing state.
On candidates flocking to dense areas, the math doesn't support it. The 100 biggest cities hold about 20% of Americans, roughly the same as rural America, and about 60% live in suburbs or smaller towns. You can't win a national majority from cities. When every vote counts equally, you chase votes everywhere, including the rural areas the current system writes off.
On Virginia, we agree and that's my whole point. Electoral votes are House seats plus two senators, so the extra House representation slavery bought flowed straight into electoral votes. That's exactly how the Electoral College carried the slavery advantage into choosing the president; a popular vote wouldn't have, because the enslaved couldn't vote.