This has always been a point of interest to me in Skyrim, though I won't read 186 pages of posts before posting myself. However, I have discussed this many time on another forum and I think I'll summarize some of the most common points in favor and opposition for each side, as well as a few miscenceptions that was rather common on the other site.
Just to give a fair warning; I am a bit biased towards the Empire, but I'll try to be as impartial as possible.
Stormcloaks:
Pro:
- Skyrim is located in a very secluded position from the Aldmeri Dominion and with two unfriendly nations on their borders the Aldmeri Dominion cannot realisticly send an invasion army.
- A Stormcloak victory would mean that the Thalmor are no longer welcome as the nation will be openly hostile towards the Dominion. Less people dragged off and tortured for worshipping Talos.
- Restoring Talos worship. Important for mythological reasons.
- Skyrim will be free of the Empire so they don't send a ot of resources to Cyrodiil. Easier to rebuild Skyrim itself.
- Passionate leader who inspires the people.
Con:
- Secluded location. While this is good when they are rebuilding their nation, Skyrims location will make it hard for the Nords to attack the Aldmeri Dominion, unless they ally with another nation.
- No guaranteed allies. Independent Skyrim is a wildcard when it comes to alliances.
- Will need a long time to prepare for war. The Imperial legion has been, as far as I understand it, the main army of Skyrim since the Nords joined in the Septim Empire. Building an army from a rebell force will take a lot of time.
Empire:
Pro:
- The Imperial Legion is a powerful fighting force even now and according to General Tullius in the Season Unending quest, most of it is currently stationed at the Aldmeri Border(to make sure there isn't an invasion).
- The Thalmors presense will be weakened by an Imperial victory, according to the Dossier on Ulfric Stormcloak.
- At least 2 nations guaranteed to be allied. The two nations who are known as the backbone of the Empire no less.
- Common border with the entire Aldmeri Dominion via Cyrodiil.
Con:
- Cyrodiil is in upheaval, according to Cicero's journal.
- The Thalmor are allowed to move very freely on Imperial land
- Continued ban on Talos worship(at least temporarily)
- Many of Skyrims resources will be sent to Cyrodiil to rebuild it, though if that is positive or negative can be debated.
- We know little about the political situation in Cyrodiil, with the exception of the unfortunate event at the end of the Dark brotherhood questline.
Misconceptions:
Ulfric is racist:
I have yet to see any conclusive evidence of this in the game. There are some sources that states this, true, but all of those sources have a motive for slander and to turn people against him. Free-Winter becomes Jarl if the Empire wins, at the New Gnisis Cornerclub you can find Imperial Armor and banner(s?).
There are some racist Stormcloaks, like Bolund and Rolff, but they are hardly representative for the side. There are also racists on the other side of the conflict, like the headsman in Solitude.
No statement from Ulfric shows that he is racist and Galmar, his right hand man, says that they are not looking for sellswords if you ask if only Nords can join(non-Nord dialogue option only) and agrees that Skyrim is home to more than just the Nords.
The Empire is but a puppet of the Thalmor:
This is how it looks at the first glance of the situation, especially if you heed the words of Ondolemhar(spelling?), the Thalmor agent inn Markarth.
However, the Thalmor Dossier on Ulfric, which I mentioned earlier, states explicitly that the Thalmors situation in Skyrim will be weakened if the Empire wins the civil war. General Tullius also states the following quote in the Season Undending quest(if you are not affiliated with the Stormcloaks and do not persuade him:
Most of the Legion is tied down on the border with the Aldmeri Dominion. The Emperor can't afford to risk weakening Cyrodiil's defenses. From the Imperial City, our war here is just a sideshow. An interlude before the main event against the Thalmor resumes.(Heard in gameplay by yours truly).
It is clear that the Empire intends to fight the Thalmor, but when is more uncertain.
X side is less moral because of Y:
This civil war has no moral supperior as far as I know. Most all things you can point out that is negative for one side, outside of the issues already adressed, are mutual. Some examples:
- Ensuring the Moots outcome by placing the "right" Jarls on the thrones.
- Execution for dissent(Jarl Skald explicitly threathens with this).
- Corruption. The Silver-Bloods and the Black-Briars for example.
- Racism. Already adressed.
Ulfric Murdered the High King:
Like the racism issue, I have still to see anytihng that makes me believe this. Even Sybile Stentor, the Solitude court mage, acknowledge that the duel not only took place, but that it was a legal duel. She says that when the duel was issued in court, Torygg was bound to respond to it.
Ulfric misused the Thu'um:
The Thu'um was given to the Nords by Kyne so they could
fight back against the dragons. It was and is an instrument of war and an ancient tradition among the Nords. Only the Greybeards code was broken, but Ulfric was no longer a Greybeard. He trained with them as a child(until he became of age and the Great War started).
So, there is my summarization of the Skyrim civil war.