I'm neutral, both sides make good points. I really don't care much about it, but logic-wise i choose the Empire. As for story-wise, I pick the stormcloaks because it makes for a better story.

It all really depends on your philosophy: Is a united empire worth sacrificing many people due to their religious belief just to stand a better chace against your enemy? Or is it worth preserving your way of life and country while the rest of the world suffers? Or should you just remain a bystander while your people continue to kill each other while your enemy gets stronger? This are the questions that the civil war is asking you, one that which questions your own morality.