Stormcloaks, though bigoted, are only guilty of letting the guy who can do the best Bill O'Reilly impression (TALK LOUD OVER YOU) take the talking stick. Racism is everywhere in Skyrim, and frankly, the Nords have every right to feel threatened, insulted, and angry at anybody that isn't a Nord, who isn't trying to help oust homeland invaders. Nords have long memories and hold grudges very well, which might be their downfall.
The Empire, on the other hand, had a broader vision at one point. They've been shaven down to a worthless and sad caricature of their former selves by an oppressive, looming regime, spread thin and ragged. They are allowed to simply exist by the whim of their cruel masters, and nothing else. They are puppets who lack the strength and have naught but broken convictions and numbers, to call them Evil as a whole is only partly correct. What the Empire used to stand for was to some degree, a touch villainous, and yet, so childish to think that all they saw was theirs to own. (Yes, the Empire is strong, but the weakness I speak of is their spirit and loss of integrity.)
The citizens of Skyrim, as mentioned earlier in the thread, the strugglers and those making ends barely meet, the Jarls who concern themselves not with women and mead, but the smaller rural areas adjoining their lands being easy targets to dragons - these are the good guys.
And, of course, Parthunaxx. If there is any true good in this game, it's him. None of us can truly know what it's like to be born fully sentient -and- with an inborn desire for power and to do wrong, nor the sense of elation coming from overcoming that kind of mountainous internal opposition, so that others might follow in his example, and search within to find their own greater good and responsibility with great power. He understands that his power is terrible and dangerous, he truly feels sorrow for the wrath of his Shout and attempts to instill that responsibility unto the Dovahkiin.
That essentially makes him like a 20 ton, scaly, Yol-breathing Uncle Benjamin Parker.