This will be my leave from this thread for some time, it's taking up to much time for me at the moment and has proven to be a source for much procrastination. I may return after some time, as I have done before.
What it comes down to is which of the factions are the lesser of evils, and given what we know about Ulfric, it's him. As Dagmar, others and myself have conveyed over the better part of a year now what it boils down to is that Ulfric is not the lesser of evils. Through his character, many malicious qualities show. And the heated discussions we've had here concerning the racism in Windhelm and the Markarth Incident, among many other things have all served to show Ulfric's true character.
The Empire has always done it's provinces well, though there have been periods of strife and crisis the Empire has endured. It is for this reason that Balgruuf is torn in his decision, for he remembers what the Empire's done for Skyrim and it's people and how Mede fought until the bitter end during the Great War. Though it's had it's crimes, the Empire's good qualities shine out the clearer in the end. Perhaps one would have to play Oblivion or any other previous Elder Scrolls title to fully realize this, but I digress, in the end, the Empire wants what's best for it's people. That is why the concordant was signed, and that's why it was denied prior to the war.
My main issue with Ulfric is not the racism, nor the debatable atrocities which took place during the Markarth Incident. My main qualm with the man is how he does not fight the real threat at hand, but the people who protected Skyrim for eras. Who is to refute this? Ulfric has the manpower and the drive to take the fight to the Thalmor occupying Skyrim, yet he chooses to wage war against the Empire. Yes, he states at the end of his campaign that the Thalmor will be driven from Tamriel. But how much blood had been spilled by than? How much chaos and destruction caused?
Pockets of resistance; not unlike the Stormcloaks, successfully drove the Thalmor from Hammerfell following the Great War. Proving that the Thalmor are not as powerful as they seem, and that the determined work of individuals can defeat them. Ulfric has the strength, the influence, the will to lead an incursion against the Thalmor as their grip on Skyrim is but less than half of what it was on Hammerfell. Yet he chooses to murder the High King, forcing the Empire's hand into the Civil War that would engulf Skyrim and ravage both sides of the battlefield, while the Thalmor sit comfortably enjoying the infighting.
In the end, both sides want to be free of the Thalmor. So why do they fight each other?