Before 2000, the last time such a split occurred was in 1888.
The gap between Trump's electoral vote lead and his opponent's lead in the popular vote is wider than the gap that existed when George W. Bush won the White House in 2000. Why? Because (as Nate Silver noted last month) Clinton had gains in large Republican states that garnered her more votes than Trump picked up by edging her out in blue states. Narrowing the gap in Texas does you no good in terms of getting to the presidency, even if it helps you make strides in demonstrating national support.
As my colleague Aaron Blake noted, Clinton's loss ironically makes it harder for Democrats to possibly change the system even if they wanted to.
Clinton's speech on Wednesday morning acknowledging her loss harked back to the speech she gave in June 2008, offering to support Barack Obama after he beat her in the Democratic primary that year. There's another layer of meaning there: Clinton lost that race because she lost the delegate count — even though, depending on how you count the results from various states, Clinton had won more votes.