Excellent article. You skillfully summarize the major points. I would quibble with one point towards the end.
The anti-majoritarianism of the Constitution was not a design flaw but a major objective of the document. The founders criticized the Articles of Confederation for being too weak. Among the weaknesses they cited, were the inability to tax effectively, the inability to regulate interstate commerce. The failure of the Confederation Congress to have a strong executive, defend the nations' borders, and subdue Native American tribes.
But the biggest fear was popular rebellions breaking out in the states. Rhode Island was controlled by a "debtors" party that sought to reduce or eliminate private debts. Madison wanted a clause in the Constitution that would allow the Federal government to nullify state laws.
The greatest fear was associated with Shays' Rebellion in Central and Western Massachusetts. Poor farmers were getting guns and shutting down courthouses to prevent the government from foreclosing on their farms. The government in Massachusetts had doubled taxes in an economic downturn. As one historian described it, "You can't squeeze blood from a rock."
Elites were terrified and rushed to pass the Constitution so the new Federal government could help crush taxpayer rebellions. American elites wanted to stop tax rebellions against themselves after leading a tax rebellion against England. One of the most notable actions of the Washington administration was building an army with ten thousand soldiers to subdue the Whiskey Rebels in Western Pennsylvania.
The Constitution was created to preserve power for well-educated elites with a national vision. They were primarily former army officers, lawyers, and merchants.
Only by eliminating the anti-majoritarian bias of the Constitution, while still preserving a system of checks and balances can we address this important "design flaw."