The Civil War in The Elder Scrolls V: Skyrim is one of if not the most contentious events in the history of the Elder Scrolls world. Never mind the fact that it's a hot button issue within the game itself, fans have continued to debate which side is in the right well over a decade after Skyrim released. Much like Skyrim's sister franchise, Fallout, the choice is ultimately in the hands of the player character, and is determined by how they choose to play the game.
When it comes to the Stormcloak faction in particular, there are plenty of reasons why the player may not want to join them, for example. These might range from political biases on the part of the player (or specifically their character), deep knowledge of the wider lore, and so on. Either way, here is a list of some of the reasons to not join the Stormcloak faction in Skyrim.
7 The Aldmeri Dominion
One thing that the Stormcloaks really seem to underestimate is the Aldmeri Dominion and its Thalmor rulers. The Aldmeri were a roughly evenly matched opponent to the Empire during the Great war and that was when the Empire was much more unified than it is during Skyrim.
If a unified Empire couldn't defeat the Elves, the Stormcloaks certainly can't do it all alone. General Tullius even recognizes this, referring to the Stormcloaks as fools for fighting the Empire when they should be fighting the Aldmeri Dominion together.
6 Skyrim Can't Sustain Its Population
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If the player pays close attention to each of the holds of Skyrim as they explore, it becomes somewhat obvious how little food is being grown around the province. Skyrim is mostly mountainous and snowy which makes much of it unsuitable for large scale agriculture. This means that Skyrim is forced to import a nontrivial amount of its food from other corners of the Empire (Cyrodiil specifically).
Without this network of trade, many parts of Skyrim will almost assuredly starve to death if the Stormcloaks are victorious, and Ulfric himself seems entirely oblivious to that fact.
5 Nord Racism
Unfortunately, much of the Stormcloak rhetoric leans on the fascist side, with many of Ulfric's supporters claiming Skyrim is for Nords only. Windhelm is a great example of where this line of thinking leads, as race relations between the Nords, Argonians and Dark Elves is openly hostile. The latter two groups are either confined to the poorer areas of the city (the Grey Quarter) or flat out barred from living in it.
Ulfric and his Stormcloaks care little for the minorities of Skyrim and would gladly kick them all out if they could. If one is role-playing as a character who doesn't share this racism (or as a non-Nordic character altogether) then joining the Stormcloaks loses its appeal rather quickly.
4 Ulfric Can't Be Trusted
It's no secret that Ulfric Stormcloak is an ambitious man. Before his time as a rebel, he was a student of the voice well on his way to becoming a greybeard. It didn't take long, however, for him to abandon his studies and use his power for the exact thing he swore never to use it for when he shouted the high king of Skyrim to pieces.
Whether this was a legal challenge is in dispute, although it's not a good look for Ulfric either way because it was a fight he 100% knew he would win due to his use of the Thu'um. His actions fit the description of a usurper more than a freedom fighter.
3 The Reachmen
The Stormcloak's central argument is that they have the right to rule their ancestral homeland independent of foreign influence. The problem is that this makes them insanely hypocritical because that is the exact argument the Forsworn of the Reach are making in Skyrim. The Reachmen (people of mixed Breton and Nordic blood) are the original inhabitants of the Reach and yet Ulfric categorically denies their right to self rule, and is even said to have violently suppressed a rebellion in Markarth - a rebellion that likely began over Nord mistreatment of them in the first place.
2 The Issue of Talos Worship
While the Nords believe very strongly in the divinity of Talos, there are plenty of other people in Tamriel that consider his worship to be absurd or even offensive. This then begs the question as to why a non-Nordic character would bother fighting for the Stormcloaks based on this significant difference in religious practices.
For example, a Khajiit would have very little reason to worship Talos since they have their own pantheon. Argonians, and the various Elf races also have their own pantheon of divines which don't include Talos.
1 Thalmor Puppetry
While exploring the Thalmor Embassy during the main questline, the player can find a dossier containing information on a few key people in Skyrim, including Ulfric Stormcloak. The dossier states that although he is uncooperative, he is a valuable asset to the Dominion's interests. This is likely because his civil war keeps the Empire not only preoccupied with conflict, it divides even further. It also makes Skyrim itself easier to invade and capture in the long run.
This revelation paints the civil war in a very bad light, as not only does it prove Ulfric is a shortsighted fool, but that the Thalmor are counting on his foolishness. A swift end to the conflict in the region (preferably in the Empire's favor) would deal a significant blow to the Thalmor's long term interests.
The Elder Scrolls V: Skyrim Special Edition is available on PC, PlayStation 4 and 5, and Xbox One and Series X|S