Your analogy is flawed. The individual "games" weren't that skewed. Instead, imagine two basketball teams play best-of-5. The scores are 100-98, 101-99, 100-101, 99-100, and 98-100. It would be bizarre to say that one team was greatly superior based on that, even though they did have a big margin in percentage of games won.
On further reflection, I do agree that the election was close. I'm guessing my previous response was conditioned on Trump being the underdog, arguing on a different point you were making.
Your "most logical analogy" still isn't quite right. The individual scores for each game were very close, and the total scores actually slightly favor Clinton. But Trump won more games, after weighting the games in a certain way. But I don't know how to do it better, I don't think there's any sport that's really played anything like this!
I'd say the best measure for closeness would be either how much of a shift in the overall vote was needed to flip the result, or how much of a targeted shift could generate a change in the result. In this case, an overall shift of 1-2% would have changed the result, and a targeted shift of some tens of thousands of votes could have. It's not the closest election ever (2000 probably takes that prize by these criteria) but it's fairly close compared to, say, 2012 and 2008.
If two countries play a best-of-5 soccer games, and one beat the other 3-0 with three consecutive 1-0 games in the last minute. It would have been hard to claim that one team isn't obviously better and the margin of winning is small.