Well in his farwell adress in the respect of the political parties and what you said, i would personally have to disagree with you. If you watched this years presidential election how often did you see republicans going after democrats on their views of abortion, gay marriage, etc. Sure there are conservative liberals and liberal conservatives, but most of our ideals are defined by our political party...that's why we label ourself as a democrat or republican. And also, his worries are justified. that's why there's so much dissatisfaction among republicans because a democrat is in office. for the sake of this answer let's assume that i'm a democrat (not saying I am and not saying that I'm not),if John McCain would have won, I would have been legitimately angry and frightened by the thought of the stereotypical thought that republicans are war hawks, etc. Republicans, same goes for dems stereotypical pro-abortion, gay rights, etc. This is just an example of the problems with the political system, that's why there's so many people hate Obama, because he's a Democrat and Republicans feel that Dems are wrong on many issues. The same thing applies during the cold war, where Republicans were the ones adding fuel to the fire in the anti-communist quest, and even called the Democratic party a "party of socialism."
Geographical distinctions definitely caused a huge problem with slavery. Pro-Slavery individuals and Anti-slavery individuals had battles simply over where one could own slaves and where one couldn't...and I'm sure you know about the South ceding from the Union.
And in the sense of Alliances, We have had a number of alliances that now we do not really want anything to do with...particulary France since they did not help with our cause in Afghanistan and Iraq...Alliances are a tough issue to tackle bacuse it's rather complicated...In World War II we were allied with Communist Russia, whom we did not fully trust, then what happened right after the war? An arms race and the Cold War and us attempting to stop Communism.
I think that, if you want to call this progress, we have progressed as a result of changing environments and the necessity of adapting to our surroundings. Sure, Geographical distinctions are not a problem now, but we pretty much had to have a civil war to settle the issue. Political parties have rather sophisticated ideals but that is simply a result of change in technology (Ex, abortions, gay rights, etc. i'm sure were not a concern when Geroge Washington was leaving office) And the alliance aspect, we take certain countries in simply out of how they prove to benifit us...this is not the only reason but it is a reason why...I hope this helps you out.