Therefore, it is clear that the Maine-Nebraska method gives an advantage to the Republican over both the current Electoral College system and the popular vote system.
Exactly. And has already been mentioned, implementing such a system nationally would likely encourage this disparity to get worse via gerrymandering.
And the rebuke there about rallies in the bronx is just silly. As if Obama finds he should rally in the Bronx, McCain might be encouraged to rally there too as obviously Obama is worried about getting enough votes out of New York to help in a national popular vote. The same could be said of McCain rallying in Oklahoma City. Obama's folks might of figured that as votes are votes, no matter where they might be, might as well try to persuade them, and follow suit.
Allot of critics of a national vote plan point to the idea that candidates would only go to big cities to campaign. Well... they already kind of do that, except its not just big cities, but its big cities in certain states. And sometimes more rural areas, but in the current makeup of political climates in the US, those rural areas are again in just the swing states.
A real national vote system wouldn't have had Obama and McCain chasing the margins in Ohio, Florida, and Missouri. You'd of seen them sweep through all fifty states and do some serious campaigning. What more, this would likely change drastically the political climate nation wide as suddenly both parties have organizations going on in all 50 states that are all essential to victory.
As for the congressional district method/proportional method in general, my final comment is that they are fake attempts to move towards a true national popular vote. A compromise designed to be poison at the end of the day, that is more likely to reward entrenched interests who hold the keys to the map room than it is to actually empower voters.