Now, with that out of the way...
The underlying conflict of Skyrim, beneath the dragons, is that the empire is on the brink of death. It faces a foe more powerful, patient and charismatic than itself, and is teetering on the precipice of annihilation. While this is going on, there is simultaneously a civil war occurring in Skyrim between the Nords and the rest of the empire. The Nords believe that they have the obligation to overthrow the Empire of Tamriel, rebuilding it in Skyrim, because the empire was not powerful enough to defeat the Aldmeri Dominion. The Nords - specifically, the Stormcloak rebels - believe that the entire empire deserved death in their defeat and that every day alive is a day of shame.
The civil war's impetus was the Dominion's primary agents, the Thalmor, being permitted to rendition away worshipers of Talos when the Dominion had outlawed the god's worship. Of course, while the empire had agreed to the outlawing, they simply moved all temples indoors and continued worshiping in quiet protest while they built up strength to overthrow the Dominion.
Then, Ulfric Stormcloak happened. Ulfric attacked the city of Markarth, which was at the time being run by the Reachmen instead of the Nords. He slaughtered every Reachman he could find and then began publicly executing every Nord man, woman and child who did not immediately take up arms against the Reachmen when Ulfric sacked the city. Ulfric then publicly demanded that the empire permit worship of Talos once again or he would kill every one of his captives. The empire relented, planning to arrest Ulfric as soon as he released his captives. Unfortunately, the Dominion found out and ordered the empire to allow Thalmor police into Skyrim to seek out sedition or the war would begin anew. The empire, unable to sustain another war without annihilation, relented.
This was the impetus for Ulfric's rebellion: a crisis that he caused, which he then says he can fix. Beyond that, he murdered Skyrim's High King even though the King, Torygg, would have gladly stood beside Ulfric and worked toward change. Ulfric's first goal in the civil war is to obliterate the neutral city of Whiterun, because as he frequently says, "If you're not with us, you're against us."
I genuinely doubt that the good folks at Bethesda intended to make a statement on the American political climate; rather, the theme seems to be to look beyond the surface. At first blush, the empire seems like the bad guys, since your character gets swept up in an Imperial ambush and captured with Ulfric, set to be executed without trial. So you go to meet Ulfric and then learn all this stuff and realize that he's the real bad guy in this civil war.
So it is with our two-party system. Beware the men who ride in on white horses who claim that they can fix all your problems. It's true that Democrats, like the Imperials, are not always right, but they're trying to keep everyone safe despite their failures. The Republicans, like the Stormcloaks, are crusading to end a problem that they created, but blame everyone else for that problem. Just as Conservatives lobbied for America's businesses to collapse, so too did the Stormcloaks wish for their entire populace to be slaughtered and enslaved rather than a surrender reached.
The Stormcloaks argued for religion when religion was never truly threatened, yet they created the very crisis against which they now campaign. Likewise, somehow the Republicans have turned this into a war on religion when no one is trying to take away religion. Conservatives have constructed their own Thalmor in their mind, some sort of secret thought police to prevent Christianity from being practiced. All the while, of course, they act to harm and outright destroy those of our populace who hold differing ideals.
Speaking of differing ideals, the Stormcloaks embody and frequently state that, "You're with us or you're against us." There is no chance for peace, no opportunity for diplomacy or reconciliation of ideals. Either you fall into lockstep or you are the embodiment of all evil and need to be purged from the earth. Does that sound familiar? The Republican-dominated Congress has been completely obstructionist, doing nothing to help the American people unless we cater entirely to their demands, at which point they MIGHT be convinced to throw us a bone of a job-creation bill or some other protection, but more than likely we won't get anything because we're not "true Americans" and thus are undeserving of any care or aid, just as the Stormcloaks refuse to aid anyone who isn't a "true son or daughter of Skyrim."
The Stormcloaks fight to chase all the other races out of Skyrim. From their own descendants - Breton, Redguard and Imperial - to the elves who have never done anything to harm Skyrim. Ulfric's father opened the gates of his city to the dark elves, since thousands of Dunmer were left homeless and destitute after natural disasters in their province. Ulfric's father was a font of charity and goodness. Ulfric segregated his city of Windhelm the moment he inherited the throne, turning the Dunmer into second-class citizens. Anyone who is not a Nord is presumed to be a seditious traitor until proven otherwise; non-Nords are often beaten, murdered, or kidnapped and tortured.
Do I even need to continue to draw parallels to the Republican party? George Romney was a man of integrity who lost his party's presidential primary because he would not stoop to the seditious and evil demands of the radical Right. Now his son stands for everything that George did not. Willard Romney upholds the principles of separation, inequality and privilege for only the few.
What I find truly amazing is that I still don't believe that Bethesda was out to convey a political message. I think they were just trying to envision the most deceitful, semi-believable militant bigots possible and put them into the game as the objective "bad" side, yet not defined as such by everyone. I'm certain that the writers for the Elder Scrolls series were just as surprised as I am that the Republican party has come to embody every evil of the Stormcloak party, from their leader to their principles.
However, just as in the game, striking down Ulfric and breaking apart his treasonous slaughter of fellow citizens is not the end of the troubles, and neither will a defeat of the Republican party in November be a full-stop win for America. However, without people trying to kill their fellow Americans, denying medical care and employment to people for not having been born into some arbitrary group, we can perhaps start to rebuild what we have lost.
Our own real-world Thalmor and Alduin the World-Eater may hover above us in the form of global economic damage and political upheaval, but if we can stand as one people we have a far better chance of surviving the onslaught than if we remain in conflict or slaughter/disenfranchise anyone outside of the Republicans' narrow definition of a True American.