I have two saves for my primary character, Ulfius the Iron--one where he join the rebellion, the other in which he supports the Empire.
When he goes Stormcloak, it's because he believes that the Empire's time has come and, like all civilizations, will pass away despite the best efforts of its best citizens--and independence is the best thing for Skyrim, no matter the birth pangs the new era must endure. His Nordic people have learned all they can from the Empire, now it's time to take that wisdom and abandon the sinking ship--even if that means facing the Dominion alone.
When he goes Empire, it's the opposite--he believes that the Empire can be saved and is worth saving, because of the benefits of the higher civilization that the Empire represents and promotes. He believes that Skyrim is not dishonored or shamed by remaining part of an international empire, because that Empire is not malicious and largely is altruistic, ultimately bettering its citizens. Despite that not every individual of the Empire is perfect, the Empire is greater than the sum of its parts, and as such is worth keeping together--especially in the face of the Dominion.
I have two saves because I see what I think is the good in each faction. Like many such instances in real-life, the decision between union and independence always involves positives and negatives with each choice--it's a matter of deciding which is the best choice in the long run. In Skyrim, I can see the good in siding with the Stormcloaks, and the good in keeping Skyrim in the Empire, so instead of wasting time trying to choose, I set up Ulfius by getting him outfitted with all the items I would want no matter the faction I chose (excepting the ones involving fun quests, like the quest for the Shield of Solitude), then made a final save. From there, I intend to pick a side, finish the Civil War first (without distraction), and then do the other when the mood strikes me. That way, I get to play both sides, and also re-do all the other fun quests in the game after I end the Civil War.
So far, I've begun the Legion side of Ulfius' grand adventure, which was very new for me, as I've always gone Stormcloak before. I'm thoroughly enjoying it, and also looking forward to starting the Stormcloak side one day. Even though it comes with a feeling of disgust from having to kill Stormcloaks, the Stormcloak side will come with the feeling of disgust that comes from having to kill Legionnaires. It's a feeling of disgust because I'm forced to fight people who, despite their imperfections, are just fighting to either maintain their civilization or for independence for their race.
Which is why I want to end the Civil War first, so I can get on with fighting actual enemies, like vampires and bandits and such.