Do you see Empire as pure bad and Stormcloaks as pure good, or do you see them as both grey?
I see as both grey, but I myself dislike the romans, (lousy, cheating, bloodthirsty copycats... Greece on the other hand.. Wait.. I am getting off topic...) so I will probably join the Stormcloaks on my 1st playthrough. But in another i will do legion.
Also, I beleive that while Alessia had the Amulet of Kings in the world and Akatosh was a symbol of order and helpfulness, the Empire was beneficial, but now, with the septim line dead, Talos' heirs no longer among the living, I think it is time that the provinces moved on and became their own seperate countries. I know people will say that if the provinces are independent, they will war with each other constantly. But I ask you, is that any better than warring with the Thalmor or Legion? Besides, even with the legion watching over them, there is all the bad things going on, dragons, Oblivion crisis, and even then the provinces fight between each other.
So my loyalty lies with the Stormcloaks.