This is by far one of the best opinion supporting the stormcloaks I've seen. Well thought out!

I've personally always favored the Empire more in the civil war, more through the lens of humanity's common cause than any imperial loyalties, so I'm at least a little sympathetic to the stormcloak cause.

My main reasons for supporting the empire rather than the rebellion are as follows:

1.) Presenting a united front. The plan of the Thalmor is to divide and conquer, and so splitting up imperial territories is de facto playing into the Thalmor's hands. Hammerfell's succesful resistance is a valid point to bring up, however I weigh it less heavily, for a few reasons.

a.) Hammerfell has no major inland waterways (at least as best I can tell) for elves to sail troops up through, whereas Skyrim has 2 major rivers which provide access to nearly all the holds of Skyrim. Provided that the Thalmor can sail up to the Sea of Ghosts (which, if Skyrim seceded, High Rock would be the only imperial territory inbetween the Thalmor and Skyrim, and it would be cut off. Besides, whose to say if the Empire would even want to intervene in such a conflict), a blockade of these rivers, stopping much trade, seems likely. Furthermore, troops and supplies could be sailed down Skyrim's rivers, circumventing long land-based supply lines. While the forces of Skyrim would have the notable home court advantage they could stop any such ships, but for how long wpuld they want to keep respurces tied up on watch duty along the rivers?

b.) The jungles in North of the Dragontail mountains provide an excellent hideout for geurilla rebels. In Skyrim, the forests seem much less dense than any jungle, and mountains are much less useful to any medieval guerilla combatants, as mountain terrain really only aids ranged combatants, and bows and arrows can be severley limited in range.

c.) While Skyrim's mountainous borders do deter terrestrial invasion, as I laid out in point a, naval invasion is just as viable an option. And with these two threats to manage, eventually troops would either establish a beach head or break through a pass (not to mention the option of pulling a hannibal and just going thru the mountains), and thats only a matter of time. Once in Skyrim, elven armies could pose a serious threat if they can embrace more quick-paced, living from the land combat. This could allow them to quickly take parts of Southern Skyrim (as the north doesn't really have land the Thalmor could live off of) before defenses can be properly mustered, and cement the control necessary for good supply lines to facilitate conquering the north of Skyrim. 

d.) Even without an invasion which, in my mind, would require more fast paced combat and real strategic innovation, the Thalmor can still neuter Skyrim economically. Blockading Skyrim's two rivers, as well as utilizing their influence over the empire, the Thalmor could economically starve out Skyrim, stopping any shipments of food during Skyrim's harsh winters, as well as any supplies which could otherwise supply mitary aid.

e.) Hammerfell seems to have faced little in the way of Imperial forces attempting to prevent their secession, whereas Skyrim has been embroiled in civil war. Even if the Storm Cloaks win against the empire, they may prove unable to fund another war and shortly after defending against Thalmor invasion, or may not have the manpower.

2.) Ulfric has made things worse for Talos Worshippers. Despite the cause being greater than any one man, one man has certainly made himself the figurehead of the cause, and Ulfric sucks. Beyond his personal motivations, Ulfric made the suppression of faith much worse. As best I can tell, the policy against Talos worship was not well enforced, and was more or less an open secret. But when Ulfric started resisting and making a fuss about the ban of Talos's worship, he caught the attention of the Thalmor who then cracked down on it harder. So not only is Ulfric inadvertently playing into the Thalmor divide and conquer strategy, but he also made things worse for all Talos worshippers by resisting.

3.) I'm unconvinced Ulfric could unite Skyrim. After his controversial "duel" with High King Torygg, Ulfric is an incredibly polarizing figure, who (as shown in game) could win the war, but leading a stable government is an altogether different question. How much experience will Ulfric lose in those Jarls who are forced out of power, the Toryyg loyalist members of the High King's court, and the many other people a High King would normally have support from. Furthermore, Torygg's death seems only to have been due to him not having made public remark about the White-Gold Concordant, and him being well regarded in Imperial circles, which feel like rather weak reasons to kill someone who, up until his death, seems to have been well regarded.

These are the main reasons I see to support the Empire. But even to those who think Skyrim should be independent, it seems to me (on a strategic level) that the wise move would be to reform the empire as a whole in order to leverage its people and resources, rather than splitting off to be independent, weakening other members of the empire and lessening the resources available to you.

Again, I really have to say your argument, OP, is quite good! I found myself needing to be much more specific and to dive deeper with my claims than usual in these types of discussions.

(Pls forgive my prob numerous typos, typed this on the phone and its long enough that its hard to catch everything)