One is elected by people not by land area. Hillary Clinton has almost 600,000 more votes than Donald Trump. He lost. The election is rigged! He always said it was rigged. He didn't tell anybody that his side rigged it so he would be called winner even though he lost.
You keep banging this drum. Why should the answer be anything other than more local government so you don't end up with a situation where you've effectively got two totally different cultures sharing one national border, each vying for supremacy over the other? If you want one set of laws for your city have at it, just don't expect the country to adopt them. If you want more freedoms in the country have at it, just expect to have a few more rules when you get into the city.
To expect one set of laws to work for the city and the countryside is absurd when lifestyles are so very different. As things stand now if you're a Republican in California or a Democrat in Mississippi you might as well not bother voting. A change to the popular vote would mean that if you live in Montana the chances are you might as well not bother voting. Presidential candidates could be expected to visit major cities and not do much else. It would hand a huge advantage to the Democrat candidate because all they would need to do would be to show up and rally the troops in NYC, DC, LA, Miami etc, while the Republican candidate who wanted to rally the troops would have to visit towns and cities across the entire country, knowing that the chances of them getting much traction in traditionally Democrat urban areas is minimal.
Since there doesn't appear to be any system that doesn't create a collection of problems, why not do away with the problem and scale back the government? Send more power back to the states so that New England and the west coast can introduce more liberal regimes and the mid west can introduce more conservative regimes. That truly gives power to the people, rather than finding that whole swathes of the mid-west are stuck with a president they didn't want for the simple reason that a bunch more people moved into the cities and voted the other way.