What people don't seem to be understanding is that this election was run, as standard, under ruling of the electoral college. If the argument is that Hillary Clinton should be named the winner because she won the popular vote, think of how much sense that doesn't make.
Donald Trump's entire campaign strategy would have been completely different. No one can say if he would have won or lost based on election run under that format. It'd be like having a basketball game, and at the end of the game you say, "You scored the most points, but we had possession of the ball the longest so we won." Nice, you won based on a condition that was only determined after you actually lost… I'm pretty confident that Trump could beat Clinton in popular vote if he's under the impression that that's how you win. His campaign would have been run very differently.
Edit: Oops, I just saw someone already made a similar sports analogy