A quick way to see this: Trump won 306 electoral votes, Clinton 232. (There were faithless electors, but we can ignore them for the purposes of this question.). Trump won 30 states, Clinton 21. For the purposes of this post, DC is a state, which it probably also should be in reality.
Each state has as many electoral votes as it has senators and representatives combined. (DC gets 3.). Imagine breaking up the electoral votes in each state into two classes: the “senatorial” electoral votes (two per state), and the “representational” electoral votes (the other ones). Then Trump won the “senatorial” electoral votes by 60 to 42, leaving a 246-190 margin among the “representational” votes.
In 2000, on the other hand, Bush won 271 electoral votes in 30 states, and Gore 267 in 21 states; the “representational” votes were therefore split as 211 for Bush, 225 for Gore. If there were, say, twice as many Representatives (870 instead of 435 – and let’s keep the math simple and say DC gets 6 electoral votes in this scenario), and every state had twice as many electoral votes, then Bush would have had about (60 + 211 × 2) = 482 EV, and Gore (42 + 225 × 2) = 490 EV. Also in this world Nate Silver’s web site is named nineseventytwo.com (which is available, as of this writing). In fact, Bush would have won with any number of representatives less than 491; Gore with more than 655; and in between, the lead swings back and forth, according to a 2003 analysis by Michael G. Neubauer and Joel Zeitlin.
In short: 2000 was the way it was because small states are overrepresented in the Electoral College; 2016 was the way it was because the Electoral College is winner-take-all.