You clearly misunderstood my post if you think I believe that Kansas has the better system than Nebraska. People who live in KS-03 who voted for Obama had their votes disregarded, but if Kansas used the Maine-Nebraska method, then the people in KS-03 who voted for McCain would have their votes disregarded instead.
But those are the two systems being compared here. One is used in 48 states, and the other, in 2.Sure, but I'm picking holes in both systems because I don't think that either of them are really any good.
One benefit of the Maine-Nebraska system, even if it didn't match up perfectly with the popular vote, is that it would make it worthwhile for candidates to spend time in places other than the big swing states. Obama had reason to pay attention to NE-02 (in fact I recall at one point the Obama campaign believed that winning that district was the key to coming out on top in a 269-269 tie they foresaw happening). A lot of districts in "safe" states would actually get some attention from the presidential candidates, since every single district would count equally.
I can agree that that's certainly an improvement, but opening up Republican localities in otherwise safe Democratic states (and vice versa) is also a feature of electoral college abolition.
What about proportional representation?
As I pointed out already, that would certainly help counter the gerrymandering issue. However, look at states with small populations. Distributing the electoral votes proportionally in states like Montana (McCain 49%; Obama 47%) doesn't really work when McCain still wins all three votes. Even in states with only four EVs, a narrow margin of victory for one candidate would still cause a 3-1 distribution of the electors.