The Electoral College, which I discussed yesterday, certainly isn't perfect. It has a number of problems, including the fact that we treat it as a ceremonial rubber stamp, and that the electors, whoever they are, were never on a ballot themselves and voters have literally no idea who they are.
But there are also problems with how the votes themselves are distributed across the states, problems that undermine a basic principle of our democracy, which is that everyone's vote is equal. Clearly, when Trump wins 57% of the electoral votes with just 46% of the popular vote, there is a mismatch.
First of all, the way that votes are apportioned by the states (in a winner-take-all manner in all but Maine and Nebraska) means that many votes in many states are worth little to nothing. If you are a member of the minority party in a non-swing state, you even know this going into election season. As an experiment, I ran some numbers to see what the Electoral College count would look like if each state instead distributed its electoral votes proportionally. Here is what we get:
Clinton: 261
Trump: 261
Johnson: 14
McMullin: 1
Stein: 1
This more closely represents the closeness of the election, although it overstates it some. Compare this to distributing 538 electoral votes proportionally across the entire nation:
Clinton: 259
Trump: 247
Johnson: 18
Other Candidates: 14
The big loser in this scenario is, of course, Trump, who benefits disproportionally from the fact that the small states (where he did well) have a larger number of electoral votes allotted (since they get to count their representation in both the Senate as well as in the House).
The beneficiary here is not Clinton, however, but third-party candidates, especially Stein, who has pockets of support all over the country, but outside of California they all get rounded down to 0 electoral votes when state's electoral votes are allocated proportionally.
Clearly, however, the winner-take-all scheme has the biggest effect here. While Clinton won more overall support than Trump, her votes were distributed very inefficiently, being clustered largely in a smaller number of states, and falling just short in pretty much every swing state. Although state lines were not drawn with this intention, the electoral map behaves very much like one that has been specifically gerrymandered to the Republicans' advantage.
Interesting to note is that the Constitution says absolutely nothing about how a state should select its Electors -- there's no reason winner-take-all should be how they're decided. However, there's also no incentive for any state legislature to change it, and plenty for them not to. For instance, while dividing up California's 55 electoral votes proportionally would result in a lot more attention to California issues during the campaign, as both campaigns now realize that votes are in play, the Democratic-controlled legislature would never do anything to let a third or more of those electoral votes walk to the other side of the aisle, not when they're basically a shoe-in for the Democratic candidate.
tl;dr - Winner-take-all electoral votes make the map look gerrymandered, and results in less democracy. But the states won't fix it individually, so we'd need some sort of Constitutional amendment (or an unlikely Supreme Court decision) to fix it.