I'm not sure what the correct answer is. Winning a national contest is always going to be about coalition-building all said and done. Trump changed the calculus on the traditional GOP coalition (going after unions -- once considered a Democrat lock), and won states he "shouldn't" have. Coalitions line up with states in a lot of cases. If Democrats started pandering to farmers (I can see this happening), the midwest might look different.

I don't see this as a "states not counting" problem as much as the issues that come up in national elections affect different populations in different ways.

If there was a national popular vote, there would still be people who feel disenfranchised because the candidates don't see their chosen issues as vital to their coalition.