You are interpreting the intention of the Founding Fathers to suit your own feelings. The introduction of the Electoral College was to prevent exactly what you are proposing — taking the voice and vote away from Americans who don’t reside in large cities and have different needs and wants they would like to have represented in government.
The cause itself is proof it’s supporters could care less about the votes of people in the rest of the country since it would only be 2 or 3 cities who benefited from your solution. The rest of the country overwhelmingly endorsed Donald Trump and the Republican Party.
Additionally, your solution would no doubt bring about an official and thorough audit of the actual votes cast legitimately in all of the states, including the ones who have made it illegal to scrutinize the tallies (why is that by the way?).
In other words, be careful what you wish for — removing the speculated 2.5 to 3 million illegitimate ballots might not leave your candidate with the popular vote either.