Yeah, They both have blatant problems but honestly, I'm more interested in seeing what they make the Dragonborn out to be in ES6. Since it's his decision how the war goes on to do, how would they decide what happens to Skyrim in that manner. If they even acknowledge it at all even.
The Stormcloaks are in it for the Nords, plain and simple. They want the right to worship Tiber Septum(I think)/Talos as they please. Keeping out Kajit/Argonians from their cities as well as others they see as inferior or untrustworthy. Sure they got the Patriotic aspect to it and that can make things seem right, but right and wrong are the same thing for different reasons.
The Imperials on the other hand, simply want to avoid the war with the Thalmor who are clearly superior in both numbers and equipment. It certainly doesn't help that they just wanted to execute you for no real reason at the start but again everyone is different. (we all can agree that that general lady is a huge jerk if not worse.) Still, both sides helped you escape Helgen, so at the end of the day it still isn't easy to say who should be helped or not.
Ultimately it's the Character's choice, and I say Character and not player because it is a Role Playing Game, and while you certainly can play yourself that's just limiting the dozens of other story-lines you exclude yourself from. It's the Character's choices that determine the outcome, and as such it would depend on who or what you're playing as.
Personally I tend to avoid that whole deal simply because it's not really my business in most cases, after all what Argonaian or Kajit would typically have personal stakes in the war?
