I posted my reasons for supporting the Stormcloaks in the Balgruuf thread, and I think someone has a link to a video that goes deeply into in his sig. I reckon that with how many blows the Empire has taken, and further n the DB questline, that their attempt to play the 'long game' with the Dominion is just utterly foolish. I also believe that the Stormcloak questline was given more time and attention. At least one of the Fort quests involves rescuing prisoners from a bloody dungeon. The attack on Whiterun is an actual epic city battle, wheras the Imperial verson is guarding a barricade outside. Atacking Solitude feels much more epic than attacking Windhelm, despite the cities history. This even extends to their final speeches; Tullius talks about pay (woo, the drama

) to a half-dozen cloned troops on a narrow pathway, and hints at coming troubles. With Ulfric you get his usual charisma, to a larger group of mixed gender soldiers in a large courtyard, and you also get the scene with Elisef, and it feels like a calm before a storm.
When it comes to the actual resolutions there is also differences. When Ulfric and Galmar win, you get the interplay wth them trying desperately to talk Rikke out of suicide, and the General who has given up, and Ulfrics point about how its more than a 'rebellion' at this point and how the Empire he knew would never have given up. If the Empire wins, Tullius gloats about slaying Ulfric, you fight them, and thats pretty much it aside from Ulfric wantng you to kill him from what I recall - rebellion put down, all in a days work, and a complete lack of drama.
Ulfric is also, no matter your views on him, a deeper and more realized character than Tullius; backstory, charisma, relevence to the people of Skyrim, backstory and all. I feel that if you are roleplaying and can justify it for the character, then you will get mor e'bang for your buck' for RP fodder as a Stormcloak.
Honestly however, Bethesda like to have a canon-storyline and generally don't make multiple endings after the mess they had to correct via Dragonbreak. BOTH sides of the conflict are correct, depending on your PC, and in the end its not going to MATTER which you pick. Somethign is going to happen on or offscreen that will render the civil war choice moot, whether that is an assassination of Ulfric if he wins, the moot simply selecting Elisef either way or another unseen contender, whether the Empire collapses due to ingame events anyway, whether the Thalmor win anyway, ect. It could be a DLC where we deal a blow to thew Thalmor that they won't recover from, be it by killing an offfcial, or a random deus ex machina.
In the end the above and my post in the previosu thread are my views on why I THINK the Stormcloaks are the better choice,
but how in the end it doesn't matter in the least.I wish people would stop calling the Stormcloaks and supporters stupid and so forth because thats just trollish and inflamatory, and defending the Empire's every choice in the past and current events while with the same breath nitpicking everything they can find about the SC. It comes across as condescending and pointless. It certanly doesn't help the credablity of a point.