You sure you understand the examples you are listing? Afghanistan and Mexico's presidents are directly elected, and all your other examples aren't democracies and hardly good examples to emulate exactly. If you want to talk what a parliamentrian system looks like, sure, but that's clearly not what you're discussing. And fyi, parliamentary systems are way simpler to understand than the EC: parties are voted on, parties internally pick their head of state. Done.Some examples of countries that do hold direct elections for their heads of state: Afghanistan, Iran, Mexico, Russia, Turkey, Venezuela, Zimbabwe..
Many democracies do not directly elect heads of state but have more complicated processes than our electoral college.
My point is that federalism is the basis of the republic, a union of states. Why should states that would not be represented as intended remain in the union? It would no longer be the system as created.
To answer your last point, the EC was never intended to artificially boost state representation. To claim that is retconning history. Systems change over time, there is no reason to be wed to an idea that is clearly detrimental to the health of a country civically.