I was always a fan of the stormcloaks myself until I tried Imperial and well... now most of my new characters end up going imperial. It might have something to do with Ulfric's axe named "Coward" but thats just how I started seeing him.
But I guess it comes down to your character and how you see him and want to develope his story.
The background I usually come up with my characters is tragic. It explains why they were crossing the border. usually seeking a peaceful life from the one they left behind. My latest orc was enjoying a freshly caught fish when the stormcloaks and imperials spilled into her camp. In the scuffle she may have pulled a blade and attacked both. She was quickly caught however and thought she was going to die a cowards death on the block. It became clear to her upon getting her freedom back that it was all a miss understanding. She was at the wrong place at the wrong time. Due to her violent background and the search for a more peaceful life, she sided with the imperials. There was "peace" in skyrim until Ulfric killed the high king. My orc believes that there should be freedom to worship any god, and that Ulfric rebelling over just one, a human one at that was simply an excuse for war.
So it comes down to how you view your character's ideals...