I think people are readding too much into this. It's a civil war. There is seldom ever a black and white good or bad guy when a nation is fighting itself. There is many layers and many issues, and people focus too heavily on just a single issue and miss the big picture. Let's explore just a few....
Legitmacy: The stormcloaks point out they're being run and administered by an outside nation; which is true to an extent, but it has been this way for 2 entire eras (hundreds of years). Imagine if today a rebel uprising formed in America where they demanded that the US government leave and cede the country to Britian (or, hell.. the NATIVE AMERICANS?), because that is how it was hundreds of years ago... times change and things move on.
Religion: The Stormcloak rallying cry is the outlawing of Talos worship, but if you speak to the imperials you realise most of THEM worship Talos too, but they do so in private and the authorities turn a blind eye to it. When you delve deeper, you also find that talos worship isn't Ulfric's real motivation, his motivations are more selfish - power and to soothe his concience.
Thalmor and the Dominion: Neither Skyrim nor the Empire likes the Thalmor. While the Stormcloaks paint the Empire as lackies to an enemy nation, the Empire themselves are clearly no friend of the Thalmor either, and are fighting a cold war, positoning their pieces on the playing field and jockeying for power with each other but keeping the guise of the treaty in place. A united Empire of Skyrim and Cyrodiil has a better chance of winning this war than Skyrim and Cyrodiil alone as enemies; the Thalmor are delibrately extending the war where possible to help keep the empire and skyrim in a position of weakness. The Stormcloaks might win their battle with the Empire, but ultimately lose the war against the bigger
existential threat posed by the Dominion.
Trade and Foreign Affairs: The Stormcloaks are highly xenophobic "Skyrim for the Nords!" as they say. This will not help them forge alliances or trade relations with their neighbours in a Stormcloak skyrim - and contrary to what patriotic individuals like to think, trade and relations are important, a nation cannot survive in isolation (See North Korea).
Intelligence Gathering: The Empire uses torture as a means of intelligence gathering... though that said BOTH sides freely execute anyone so much as suspected of working for the other side.
Next time you're tempted to name one side or the other as best on a SINGLE issue think how many other issues exist
