Have some claps. I like your thinking, and I side with your overall point, but I think you need to dig deeper into your breakdown, and then you need to step back a bit and think deeply about the entire point of the Electoral College.
First major error is presuming all the Libertarians would vote Trump. Libertarians are very mixed on who they would have voted for, with a gun to their head. Trump is very, very authoritarian. Most of the Gary Johnson voters I know would have written in Harambe, or simply stayed home. There were a large number of libertarian leaning voters who were scared into voting for Hillary or Trump by the general level of freakoutery, so I don’t think it’s fair to dump the remaining ones brave enough to vote third party into either of the main party buckets.
So if you strip them out, or apportion those among both main party pools by a more objective ratio, maybe the “Hillary won the popular vote” case is buttressed more. I think stripping them out might be a better choice, and I also think that some of the Jill Stein votes should be stripped out as well, as many of those were protest votes against Hillary’s actions in the primary. They also were likely stay-at-homes or Harambe write-ins.
Now here’s the converse.
The Electoral College exists for a very specific reason. Rural states did not want to join a union of states where their voices would be marginalized, and if the architecture of the voting system was rigged in such a way that their state would have no say, they never would have joined the United States in the first place. There’s an argument to be made that first past the post, winner take all state apportionment of electoral votes is a bad way to do it, and that argument is deeply rooted in mathematics:
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…but there is no good argument to the idea that we should shift to a popular vote where a tiny fraction of the United States geography can bully the central “fly over” states into policy that does not work for their region. At a minimum, the best you can go with an honest “fix” is to apportion electors by vote ratio within each state. And when you do that, Trump still wins because a vote in Montana is worth more than a vote in California, as it should be.
When I hear people clamoring for a return to the popular vote, I see that as a giant bait and switch being played on the rural states who joined the union under very different pretenses. If that were made, it should at a minimum be accompanied by an opportunity for any state which does not like the rule to peacefully exit the union.