Ya know, the more I think about the events of Skyrim, the more I realize how badly an Imperial victory could actually go for everyone.
First lets consider Tullius. Man is a brilliant tactician, and is no fan of the Thalmor. Which is why, no matter who wins the civil war, I suspect he's never going to see Cyrodiil again. His usefulness in putting down the Stormcloak rebellion is over, he's now a greater threat than an asset in the event of a second war between the Dominion and the Empire, which he does indeed plan to undertake at some point and the Thalmor likely know this.
He's a dead man walking. It would be so easy to ambush him and his men as he returns to Cyrodiil and blame his death on vengeful Stormcloaks, or simply hand said vengeful Stormcloaks all the info they need to kill him themselves.
Next we need to consider the death of Emperor Titus Meade II as a result of Amaund Mortiette's hiring of the Dark Brotherhood to kill him. Amaund is a scheming, conniving, power hungry man. The exact sort of man for sale to anyone who can further his aims. People like the Thalmor, for instance. If the Thalmor offered him their discreet support in becoming the next Emperor they would have a ready made puppet to keep the Empire nice and neutered, especially if they ever discover his involvement in the death of the Emperor. A nice little Sword of Damocles hung over his head in case he ever decides to get uncooperative.
So yeah, much as I think Ulfric tends to be a douchebag somehow I think this is a situation of "He may be an asshole, but he's our best shot."
I used to think that the Empire was the best choice, but my mind has been made up with the Stormcloaks. They're not racist, look at Riften and Morthal under their control. The Dark Elves in the Grey Quarter are just too proud for their own good and victims of bad writing, there seems to be inconsistencies in how soon they wanted to portray Red Mountain's Eruption. Ulfric kept the Argonians out to keep them from fighting with the Dark Elves. It irritated me that some of the Jarls are absolutely incompetent on both sides, and I think the Dragonborn should have had more influence in picking/changing some of them. In my latest playthrough, I installed the mod to let Balgruf side with the Stormcloak Dragonborn and used console commands to change the Winterhold jarl because I can't stand him. Ultimately, I find the Stormcloak Jarls to be better picks as a whole than Imperial aligned.
I think you've got Amaund's motivations potentially wrong, he hinted he wanted Titus Mead II gone for various reasons, namely to strengthen the Empire and bury his incompetent bureaucracy, at his own personal gain as well. I also think Amaund was a middle man of some kind, acting as an agent for someone we will later discover. I don't think it will matter though, the Imperials are not destined to come back with the strength they once had. If anything, they will fortify their power in Cyrodil, and the other former provinces do not want to be under their control. The Septim Empire is long dead, as is the Mead. If anything, the other provinces may be Cyrodil's ally, I don't even think High Rock wants to be a part of the Empire other than trade.
I really hope the Thalmor and high elves in the next installment are less "generic smug boogeymen" and actually have some personality or moral ambiguity, perhaps with in-fighting. Hopefully High Rock and Hamerfell: Electric Boogaloo 2 will be done justice.
Gonna add a few cents of my own here:
Concerning Tullius; yeah, it's pretty clear that the guy is screwed no matter what. He's an excellent tactician, which makes him a massive target for the Thalmor; given how open everyone is about how there's going to be another war with the elves at some point, it makes sense that the Thalmor would want to eliminate anyone that could realistically fight against them.
And yeah, the Empire is pretty much done; even in Oblivion, I think it got mentioned that the time of the empire was more or less over, with there needing to be a new government some time. That, and the events of Skyrim really do not help in this regard; while you can destroy the Dark Brotherhood, thus keeping the emperor safe at that point, it's unknown/unlikely that is canon to the series. Meanwhile, it gets made clear that the empire already has only a small amount of its original territory and power, and that the elves already kinda have a stranglehold on the Imperial government; it's kinda unlikely that the empire would really be able to move against them, realistically.
Concerning the Imperial Jarls of Skyrim; it's weird how many people seem to miss that several of them are already in bed with the Thalmor. I mean, it gets made pretty clear that, if you side with the Imperials, then you've effectively given control of Skyrim to the Thalmor by proxy: Siddgeir of Falkreath, Maven of Riften, and even Queen Elisif and Thane Erikur of Solitude all seem to be supporting the Thalmor in some way. Doesn't help that, according to cut content, Balgruuf and Elisif were both supposed to be killed originally, the later by the Thalmor-supporting Erikur even!
Also, I agree that we should have had more influence with the jarls; I get that the point of the civil war was to show that both sides had valid arguments, but the assholes on both sides are... annoying to work with, to say the least.
There's also the issue with people constantly whining about the Stormcloaks being "racist"; seriously, TvTropes tries to use the current situation in Windhelm as an example of how Skyrim would "obviously" be if they won the war. The fags keep forgetting one key detail;
it's all during a massive civil war, with the economy being drained and the Nords being naturally wary of outsiders during a conflict. Not to mention, most of the other races have rather valid reasons for the Stormcloaks to be racist against: the Khajiit tend to be thieves and their country is allied with the Thalmor, the Dark Elves have a history of slavery, the Argonians run the risk of potentially fighting with the elves in Windhelm, the High Elves are the primary population of the Thalmor, and the cult tends to recruit people of all walks of life. If anything, the Stormcloaks come across as fairly realistic; only a braindead moron would be trying to open their borders in a time of massive upheaval like this.
Seriously, do any of the fags on Reddit or TVTropes have even a small grasp of politics? Actually, come to think of it, that's probably what they want; given the number of freaks that seem to seriously believe that the Thalmor have the "right of a superior species" to destroy mankind - the Elder Scrolls fandom is full of fetishistic misanthropes, I've found - it makes sense that they would try and weaken their enemies through manipulation and attempts to eliminate Talos. Also, the constant focus and acting like "muh racism" is the biggest problem and factor in the series is ridiculous; the Thalmor are literally trying to destroy existence, and yet they're really saying that it's a good thing because it would mean that there "wouldn't be any more racists"?
Also, I hope we get some more nuanced Thalmor in the next entry; ESO showed that the Thalmor used to be fairly reasonable by comparison to the Skyrim elves, so it makes me both wonder how the group went from one to the other, and it makes me hope that a more moderate/reasonable faction of elves can show up in the future. He's hoping Bethesda doesn't bend the proverbial knee and completely screw the plot...
