The rebellion in Skyrim is a huge blow to the Empire.
On the other side, the Imperials are desperately trying to maintain their remaining strength so can prepare to fight the Dominion again. The Nords respect strength and honor, and in their eyes, the Empire no longer holds up to those principles. The Stormcloaks are fighting for independence because they feel the Empire abandoned it's people and became a puppet of the Dominion by signing the White-Gold Concordat that, among other things, banned the worship of the hero-god of man, Talos. On the surface they both have faults, but their core message is equally justified. I suggest you look further into each side's motives. There is no third option that ultimately completes the questline. I don't want to spoil anything, so I'll just say you can either choose a side or ignore the war.