Ah, the mighty question of Skyrim. This is the one that caused so much fights it almost became a taboo in chat. Well, I will say, with reason, why I side the way I do.
First off, Ulfric and Torygg's fight. The Stormcloaks say it was a duel, the Imperials say it was a murder. Given what Torygg tells the player in Sovrnguard, he did have a chance to defend himself.
- "When Ulfric Stormcloak, with savage Shout, sent me here, my sole regret was fair Elisif, left forlorn and weeping."
- "I faced him fearlessly - my fate inescapable, yet my honor is unstained - can Ulfric say the same?"
Now, with dialoge from Sybille Stentor, We can start to see the Duel/Murder of High King Torygg was unnecisarry, and Ulfric was more into taking the throne than succeeding from the Empire. She states that Torygg, if asked by Ulfric, may have stood up against the Empire. Skyrim could have succeeded peacefuly, like Hammerfell did long ago. Instead, with the killing of Torygg, war sparked. The civil war began.
Second topic. The white-gold treaty. The Empire was beaten into submission by the Thalmor, and in this fight fought Ulfric. The white-gold tower fell, and a treaty was signed. There was two choices.
A. Be eradicated and replaced. This would have affected all proveninces terribly, and change every event from that point on. Everyone would be under the forceful rule of the Thalmor
B. Sign the treaty. Though the Empire would have to adopt some Thalmor/Aldmeri Diminion laws, they would stay intact. While this also affects everyone, it would be far, far less so.
The second choice was the obvious answer.
Third topic: Talos worship. Talos is used by Ulfric and the Stormcloaks as a recruitment tool. It is very likely that they hardly care about it in the first place. Talos, being an entiamorph of three people (Tiber Septim, a Cyrodillic hero. Zurin Arctus, the first battlemage. Wulfried, the high king at the time), they have a 1/3 reason to care for him. Though it is not known if Talos is aware he was these three, or if he has his memories, it still stands. They use Talos the same was America used the idea of being bombed in the mid 40's.
Forth topic: Tullius and Ulfric. Tullius is subject to much hate, at the game presses you from very early on to join the Stormcloaks (Thanks, intro), but he never really messes up. If you do play the Imperial quest line, Tullius shows a string of good judgement and well focused mindsets. After you win the war, he says he suspects the Empire will go to war with the Thalmor soon, showing he in fact does not agree with everything the Thalmor pretain too. Legatte Rikke, who is a sort of house carl to Tullius, is a Talos worshiper herself, which shocks Tullius, but he never once tries to change the fact. Rikke and Ulfric most likely served together in the great war, as after Ulfric's death, she says "Ulfric my old friend, what have you done".
If you played the Stormcloak questline, with his dying breath Tullius concedes Ulfric and the Stormcloaks had a point regarding the decadence of the Empire and the uncertain future Skyrim faces, but with his last words he claims the Imperials are not the villians and warns Ulfric that the war ultimately benefited the Thalmor the most.
Many times trough speaking with a variety of NPC's, Ulfric is shown to be a man of greed. Killing Torygg for the throne was the first step. This is a man who would do anything for personal benifit.
Fifth and final topic:The future.
With the Empire: Skyrim will stay part of the Empire. A war with the Thalmor will most likely be waged. With the size of the Empire, and if enough time has passed, power, they have a chance to defeat the Thalmor. This will bring an end to the ban on Talos worship, the adopted Thalmor laws, and the unethical ways some thigns were done. The entire coninent of Tamriel will be affected, most likely negitivily at first, but later possitivily. If you take MK lore into the Bethesda lore (Most do not, but a very small few do) this is the end of Landfall, with it being avoided.
With the Stormcloaks: Skyrim will no longer be part of the Empire. You now have a weak Empire and a weak Stormcloak rebellion. The Thalmor/Aldmeri Diminion will war with them, defeating the weakened Empire with ease. Though, unlike the Empire, the Stormcloaks have more of a chance to make allies, the Thalmor is large enough to defeat the singe-provenince rebellion. If you follow MK lore with your Bethesda lore, this is the begining of Landfall, with it not avoided.
Conclusion: The Empire is the better choice. It will benifit everyone better, and every reason you have to dislike them would be gone after the defeat of the Thalmor/Aldmeri Dimionion. Skyrim, the Empire, and even the independant bottom half of Hammerfell.
Tullius is the simpler choice of the two main faction members, and less corrupt than Ulfric in every way.
Out of the two factions, only the Empire could defeat the Thalmor/Aldmeri Diminion.