Well said.
There's a lot of exaggerated language in this debate, as we have a tendency to take the colorful words of the various leaders and repeat them here. But effective speeches are rarely made up of sound arguments. I like the fact that you're avoiding such language in this a post. It's refreshing.
In that regard, I don't think reasonable SC supporters really argue that the Empire is literally being controlled by the Thalmor, only that the Thalmor influence is sufficient enough to cause real grievance.
Likewise, I do not believe that the position of reasonable SC supporters is that the Empire literally controls Skyrim, only that its influence is great enough to be experienced, that it does affect the choosing of a High King, that it does affect the raising of an individual to the position of Jarl (to wit: Siddgeir), and that it does this without giving any similar influence back to the people of Skyrim over its own internal politics. In other words, Empire influence affects Skyrim politics, but how much say do Skyrim Jarls have in Empire politics? I would say they feel they are getting the short end of the stick here.
This may not feel like much of a beef, but in politics the jockeying for a tiny bit of power here and a minor change of laws there dominates most of history. After a few long decades of this sort of power struggle, the accumulation of tiny grievances can blow up, and if it's accompanied by popular support, it may turn into a rebellion.
Not all the grievances are tiny, however. I find it hard to believe that question of religion gets such short shrift, as though the symbolic meaning of a law can carry so little weight. This is not my understanding of how the hearts of devout worshippers beat. People will riot over the rumor of a single instance of a holy book burning on another continent. It is easy for us to dismiss this as either the machinations of a power-mad cleric or the response of a crazy bunch of zealots. But given the degree to which the question of religion has dominated politics for thousands of years, even resulting in schisms based on differing arcane interpretations of the same text, I would say that it's more likely there is something fundamental to the functioning of the human heart that makes our struggles over belief so deeply bitter. I do not think the citizens of Skyrim are immune.
I do believe that I was one of those who asked, if not now, when? in regards to the 25 year wait for the Empire's re-engagement with the Thalmor. I don't get the impression that the Civil War has been going on for that long. I understood that the event that precipitated the mobilization of Legion troops in Skyrim was the death of King Torygg. Prior to that, the Empire would be aware of an increasingly loud voice iterating the grievances of those who support Jarl Ulfric (remember he talked at the last Moot about independence in tones "just shy of treason" -- as Sybille Stentor put it), but I didn't think they'd sent any troops to quell those voices until after the High King's death. As a result, I did not get the impression that the Civil War had been weakening the Empire for this entire duration.