For the Empire!
For The Stormcloaks!
The empire might have lost the war, surrendered to the Thalmor and left in shambles (kinda). However, the Stormcloaks are not the answer for a couple of reasons: 1. Ulfric is indirectly assisting the Aldmeri dominion with his rebellion, hindering the empire from developing ( and was allowed to do so by the Thalmor, as we see in the Thalmor Dossier ). 2. Ulfric pointlessly killed the High king, elected by the moot of the jarls (Ulfric himself also voted for Torygg ). In the game we actually learned that Torygg respected and liked Ulfric, so if Ulfric had gone and asked for independence, Torygg would have probably obliged. 3. Lets assume that Skyrim "gets liberated", what would happen next? As we can see in the Thalmor Dossier (pardon me I do not remember which, feel free to search for yourselves) the Thalmor are willing to cooperate with whichever side wins. The Stormcloaks however, will most likely refuse to cooperate with them, this can lead to (1) war, in which all of the Empire, will be forced to march to reclaim Skyrim since the Dominion is just not willing to waste resources on the matter. (2) The Dominion will simply charge in, wage war on the Stormcloaks, and judging by the Dominions military prowess they WILL succeed. Thusly giving a big chunk of Tamriel to the Dominion, reinforcing an already powerful opponent. On the contrary, I sincerely believe the empire will be the better choice because, if the empire gets reunified, without the political conflicts. They stand a chance of amassing their strength to take the fight back to the Thalmor
The Empire was in a tough spot. They didn't want to surrender to the elves any more than the Stormcloaks did. But rather than foolishly allowing themselves to be slaughtered for refusing, they went with a craftier longterm solution: Agree to peace now, give in to a few provisions, and then bide our time as we quietly amass our strength and wait for the right moment to strike. All the Empire asked of its citizens was to try to understand, play along for a little while, and temporarily give up the open worship of Talos in exchange for unrestricted freedom in the future. But that wasn't enough for some people (ie, the Stormcloaks), who like petulant children made the decision for everybody else because of their selfish desire to have their own way RIGHT NOW. This thrust the already weakened country into a civil war - a decision that gave the enemy an even greater advantage - and sowed discord among the citizenry for years if not decades to come. The Imperials were willing to restrict certain public freedoms (while still encouraging their private use) temporarily in order to secretly prepare actions that would defeat the enemy for good. The Stormcloaks didn't want to give up anything for any length of time and didn't care if they - or anyone else - died as a result of their wishes. I find the Stormcloaks' argument to be very selfish, shortsighted and foolish.
Talos is recognized by Akatosh who says "Serve and obey your Emperor. Study the Covenants. Worship the Nine, do your duty, and heed the commands of the saints and priests." (Ten Commands: Nine deities) I don't know about you, but I don't want to go against the chief deity of the NINE gods.
I originally wasn't going to choose a side, but after seeing the execution of Roggvir in Solitude after helping Ulfric leave the city after a (legal) duel with the now dead High King Torygg, then condemned by the Empire as a murderer, I felt compelled to take up arms. While I agree with the Empire signing the White-Gold Concordat, knowing their weakness, it wasn't the best thing for either Hammerfell or Skyrim (Hammerfell was supposed to cede large territories in the south to the Aldmeri Dominion, and Skyrim was not allowed to worship their most revered god). After Hammerfell elected to continue the fight without independent of the Empire, and WON, it became clear that the Empire, once strong and capable of defending itself from the threats was now but a shadow of its former self. It is true that should the Stormcloaks win, they'll face an invasion of elves, but they, in their home and under the leadership of a ruler with just Skyrim's interests in mind, stand a good chance of turning the Elves back as Hammerfell did. I think many who fight for the Stormcloaks don't particularly hate the Empire, seeing as it was built by their forefathers under the ruler of Talos of Atmora, but they can no longer see any benefit of remaining in an Empire that's ruled by an Emperor so far away who can't cater to Nord needs and desires when a High King ruling an independent Skyrim can. Of course, it's a risk. The Aldmeri Dominion has had 30 years to recover from the Great War, and so has the Empire. But Nords on home soil (which is very mountainous and cold, making invasions dofficult) is a lethal combination, especially with their style of fighting being so different from the trained and disciplined Legions, but very effective.
I played as a Nord, I cannot side with the foreign invaders. Also, it is morally wrong to side with invaders. I play in a way that makes sense (to me at least).
Honestly, either way, it's better than just leaving it alone. You can find evidence that the Aldmeri Dominion plans to keep the war going, and plans on invading Skyrim when it's weak. But seeing as the Empire is crumbling to pieces, and, though it doesn't have to be the Dragonborn who does it, the emperor will be assassinated, independence is the best route for Skyrim.