Statistically, 3 million isn't a huge percentage, although it is significant although various sites show different totals. The BBC site shows about 1.3 million, 47% to 48%.
What I would be concerned by is when a candidate receives a major % of votes cast from one party but EC going to the other, in many states. Many states had a very small percentage difference but one thing stands out- cities vote predominantly Democrat, outlying areas mainly vote Republican and neither group wants the other governing them.
It's not as simple as saying "OK, we're no longer going to use the Electoral College".
OK, if Washington DC, California, Illinois, New York and a couple of other places cause all elections to go one way because they have more voters, expect a lot of people to move, or leave the country. Look at the way those places are run and you'll see why they shouldn't be the only places to determine the outcome of elections.
Based on county and state vote totals, Trump kicked Hillary's ass and if 40 states essentially have no say, expect some serious pushback. They both had some huge margins of victory but most states were far closer.
https://www.bbc.com/news/election/us2016/results