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Well, the civil war in Skyrim is just strange. It seems like they're trying to create ambiguity, but at the same time, Ulfric and his followers are portrayed as outright villains. Among the positive aspects, one could mention the escape scene. In that scene, the Empire looks particularly bad. And also the Riften incident. But among the negative aspects, one can recall their nationalism, Ulfric's megalomania, his behavior in the council, and the fact that, due to them, the Thalmor arrived in Skyrim. Or the incident in Whiterun, where he refused to duel with Balgruuf, instead deciding to drown the city in blood. One can also recall their emphasis on "cultural traditions," in contrast to the beneficial influence of the Empire. There's a lot, in general. And again, returning to the Thalmor. What does the Empire do? Reluctantly, they agree to the terms, intending to regain their strength and strike back at the Altmer. What does Ulfric do? He weakens both his beloved Skyrim and the Empire, which is exactly what the Thalmor wants. To be fair, if you first complete the Empire questline and then the main storyline, the defeated Ulfric in Sovngarde admits that he was an idiot. But not because he weakened the Empire, but because of Alduin.
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In short, even Dagoth Ur is a more ambiguous character than Ulfric. Although his goal is similar, and his methods are even harsher.