You said Clinton’s message “...just didn't click with a lot of people. Trump's did.” That’s a numerical comparison. Are you saying that X > X+3000000? It’s an incoherent claim, so find another argument.
It's only irrelevant for deciding who wins the office. You are making the argument that Trump won because his arguments were more popular among the electorate, which is provably false using the popular vote total.
Hillary Clinton's message resonated with over 3,000,000 more voters, however unfortunate their distribution was.
Insofar as the presidential election is concerned, the electorate is the 538 people in the electoral college. Trump was more popular among the electorate not HRC.