As far as I can tell from Wikipedia, only five elections have ever been won by someone lacking a plurality of the popular vote. Three of those cases happened before 1900. If we look only at the more modern examples, the Republicans have won the presidency but lost the popular vote twice (2016 and 2000) and the Democrats have never done this. In fact, this is a true statement over all of time, but once you get back more then a century the political parties are so different as to make the comparison meaningless.
That is to say: the Democrats have never had a presidential election that they won without winning the popular vote. I do not love the two party system either, but in this case it doesn't feel fair to say that both parties are currently equally benefitting from the Electoral College.