So, as many of you know I am a huge supporter of the Stormcloak rebellion. However, I think it should be noted not everything the Stormcloaks do are right. And, I want to get rid of this notion Imperials seem to have, that I think the Stormcloaks are the best.
The Stormcloaks and Nords have issues with Alcohol and other intoxicating drinks
This is true, the Nords have always been big on having good ale before a battle. The Stormcloaks would likely be no exception, and Alcohol does not really do good things for soldiers who are supposed to follow orders and whatnot. This could mean, leading charges, protecting towns, and all that would be much more difficult if a huge amount of the soldiers simply drink constantly. It also might mean the soldiers are just overall less competent in all tasks, the Imperial Soldiers don't seem to be as into it, therefor, the Legion would likely not have these issues
The Stormcloaks ruiling Skyrim would not start with any nations on their side
The thing is, if Skyrim becomes independent, the other Independent nations are probably not going to jump on their side very fast. It will probably take some political shifts, signing agreements and concordats, etc, which does take some time. Leaving Skyrim indpendent, without trade of allies, and open to a possibly return of the Legion or the Dominion! With the Empire there would be ensured three allied nations to deal with whatever comes.
The Stormcloaks started conflict in Skyrim!
Even though, I don't believe they started the fighting. It is kind of undeniable they did start massive political turmoil within their province, one can say it was for a good cause. But even then they still did start something that would later become a brutal war. Some may have wanted to simply have peace, as Jorah said "common people pray for rain, health, and a summer that never ends. They don't care what games the high lords play".
It might cause years of great teamwork to turn into a bitter rivalry of nations
We shouldn't joke to ourselves, the Empire likely would not care for Skyrim if they did succeed from them, even if they did outlaw their religion they could argue Skyrim left in a time of need. Even if the Stormcloaks manage to calm Tamriel down, the Empire would most likely be upset with Skyrim for that Civil War and possibly turning the Empire to nothing (an Empire needs to be more than one province, or else it is just a nation). Which would mean, the Imperials and Nords, who for long were good Companions, could now just dislike each other, meaning Skyrim would have lost someone formally they would have been able to consider, an allied country.
Now, stop saying I always glorify the Stormcloaks, I admit they have some issues, and that the Imperial Legion is NOT all evil. But, overall I feel the good is stronger than bad, and that the Stormcloaks would do some good for Skyrim, more so than the Empire.