In Skyrim, the black and white moral motivations of most games have been replaced by difficult choices and painful consequences. No matter what you do, someone is going to think you're a jerk.
I remember realizing the Stormcloaks were dicks just like the Imperials...it was pretty surprising, and it has pretty much stopped me from continuing either faction's quest line.
i didn't really care, IMHO it's just about the money and the items you get for finishing their quests :)
Everyone is a dick in their own way. They just want you to choose which side you believe in. The stormcloaks, believing that only nords should rule skyrim, and kind of not wanting racial equality in skyrim. The Imperials, wanting to rule all of tamriel, with a lot of corruption in their ranks.
I think the takeaway here is "just kill everyone."
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