Both sides fight for dominance in Skyrim.
Both sides revel in killing the other.
Both sides replace the jarls of enemy holds with whomever will obey them(even with criminals, like the Black-Briars and the Silver-Bloods)
Both sides resort to blackmail and thievery.(Riften & Markarth)
Both sides make accusations of crimes against the other.
Both sides will eventually lead to a supremacist movement or Ethnic cleansing in Skyrim(for the Empire, it's the Thalmor wanting High Elf supremacy. For the Stormcloaks, it's them wanting Nord supremacy)
Even the quests are all the same. Same goals, different locations.
And the Thalmor don't want either side to win. The continuing conflict keeps both sides weakened and vulnerable, but either side winning means both sides will be able to marshal their strength and would probably ally against the Thalmor later despite differences(the enemy of my enemy is my friend.)
So all the debating over which side is more legitimate than the other is completely pointless. Both sides have the same qualities and faults with a different face. Only difference is whether you prefer to wear leather or a bear's head.