C'mon, I know you were missing these.
But in all seriousness, I've always been on the Empire's side but these days I can't tell which side is better anymore.
I'm currently playing my Nord Dragonborn for the third time, and since he is my main I can't have him join a side I might regret later.
So, I'm leaving him for last. After I've played my remaining characters I'm keeping on hold (some joining the Legion and others the Stormcloaks), I will finally make up my mind on where he should stand.
I'll start with my cons.
Personally, I don't see any great reason to distrust those who say that lust for power, as the filthy thing we know it, is the main motive behind his ambition.
I also have yet to see an argument that could convince me that the Argonians situation in Windhelm is justifiable. Some speculate Ulfric is concerned about them, but I need to see canon evidence, as in npc statements.
Others say they had it coming, but living in misery can drive you into thieving. And the way Scouts-M.S. puts it, it seems to be motivated by anger at their employers as well.
The Dunmer subject is more open to debate since some non-Nord citizens think they should try to earn the Nords trust instead of complaining, but I don't see how they're lazy or why they're supposed to join such a Nord centric war.
The pros: It seems to me that Bethesda really may be taking the End of the Empire route. In the DB DLC, Adril Arano tells you that Morrowind was abandoned by them during the Oblivion Crisis. It's funny because this fact didn't exist prior to the DLC, so Beth didn't really need to add yet another province among those that hate the Empire and another crime to the Empire's record.
And I don't think Ulfric is faking his Thalmor hatred or his passion for his homeland. So to a certain extent, I believe he's fighting for what he claims to be.
The accusation of murder clearly isn't true, as even Sybille Stentor confirms that it was a duel following Nordic tradition.
Sometimes I find that Stormcloak followers like Roggvir, Ralof and the Greymane family draw a lot of sympathy as well.
Still, I don't agree with Ulfric's attitude in certain moments, namely his bullying of Elisif (Season Unending). There is no honor in mocking your slain enemy's widow. And after taking over Solitude, Galmar comments on the part of the speech where he says he can't take the mantle of High King, like "well played".