The main reason for the difference in millions isn't even electoral college per se, it's the fact that most (all but 2) states allocate all their electors to whoever gets more votes in that state. In essence, every state throws all its minority votes away. If you think of it in terms of vote suppression (which, frankly, it is), it's one of such epic proportions that it dwarfs everything else, including redistricting, voter ID laws etc.

I mean, think about it. In California, 33% of residents voted for Trump this year - and those votes didn't count in any sensible way. In Texas, 43% of residents voted for Clinton this year - and those votes didn't count, either!