Oh boy, who do I side with? Good job Bethsda for making there be no right answer.
Personally, I would go with the Stormcloaks. Long-term wise I think they're the best choice. Short-term wise the Imperials are.
Here's my analysis of the situation divided into all the major players and what they want and what their motives are. Feel free to comment.
The Thalmor: At the core, these guys want anyone who isn't a native race of Tamriel dead. The only thing holding them back is how fast they can do this and get away with it. For them, the civil war in Skyrim is a good thing. It pits a whole bunch of humans, most of whom are good at fighting, planning and leadership, against each other and a lot of them end up dead. And the Thalmor aren't even to blame and don't even get their hands dirty. It also gives them more time to go after the people who don't fight in the war. If the Imperials win, humans won't be killing each other off, but the Imperials have a treaty with the Thalmor and aren't in any shape to oppose them. So the Thalmor's goals will just take longer. The worst thing that could happen is for the Stormcloaks to win. Then not only are humans not killing eachother, but the Thalmor will be driven from Skyrim and they won't have any influence there at all. This also frees up Skyrim to ally with other countries who don't like the Thalmor as well, like Hammerfell. Also, the Thamor have been planing this a long time, they just need a opportunity to get in power and the Obivion Crisis give them one. And if you do beleave everything you read, it's not just the humans the High Elves think are abominations... I don't like where that could lead.
The Imperials: These guys signed a treaty with the Thalmor (Aldmeri Dominion, they're pretty much the same to me) that runs along the lines of "do what we want you to do and we won't slaughter you all". Where do what we want you to do equals, no worshiping Talos, letting the Thalmor do whatever they want and no resistance groups. On the plus side, everyone gets peace, on the negative side, how real is the peace with all the Thalmor sneaking about. What makes the situation even worse is that the Imperials don't like the Thamor either, but they obey them anyway because the Thalmor are currently more powerful then them, so the peace is a very flimsy peace. The way I see it, there is no "good end" for the Imperials. If the war goes on, more of them die. If they lose, and the Stormcloaks win, they'll have to come to terms with the fact that someone did push the Thalmor back, as well wondering where they stand with the Thalmor. If they win, they will have to keep peace in Skyrim, which probably won't be that easy (because I have a hard time seeing the Nords only having one rebellion against the Thalmor). They'll also have to deal with what the Thalmor want the Imperials to do after they take over Skyrim.
Stormcloaks: These guys are the most straightforward of the bunch. Someone invaded their home and told them to give up centuries of tradition and they don't like it. The only thing really complicated about them is their leader. They can get both the best and worst endings as well. If they loose, they all die (and someone else follows their example?). If they win, the Thalmor are out of Skyrim. Then they'll have to deal with keeping peace in Skyrim, but at least they won't have the "who is really in charge here?" feeling the Imperials do. As far as the long-term future of humanity goes, you can't get much better then this.
Ulfric: When it really comes down to it, this guy reminds me of Talos. Both Nords, both can shout, both are fighting against elven invaders, bothe are leading large groups of people etc. One big difference I do see is that while Talos wanted to take over all of Tamriel, Ulfric just wants the invaders out of Skyrim (as far as I could tell). His big flaw is that he's racist. That said, eveybody in Tamriel has this issue to at least some degree, so it's a social norm, and Nords seem to have it particularly bad (Kadjiits anyone?). For me, it's also a very weak argument against him as the Empire dealt with this a lot and it was only towards the end of the 3rd Era that it became the way it is in Oblivion, that is, every race is as equal as any other race. (Anyone think what it wouold be like to be one of the elven races at the time of Talos?) The strongest case I can make against him is that we don't know what he is going to do yet with being High King of Skyrim, whereas we can make a good guess as to where the Thamor and Imperials are going. I'd say he's the the lightest of three grey paths to take, at least if you want the human races to have the best chance for survival.
Speculation
You, the player, have a talent for Shouts. The Greybeards are not dragonborn (as far as I can tell), but they can also use Shouts, only with a lot more training. Then you have Ulfric, who can uses Shouts also, but is not the type of person who the Greybeards would train. So where did The learn how to Shout? He can't be dragonborn as then he would have to kill dragons to unlock the Shouts... if I'm missing something I'd like to know.
From what I can tell, being dragonborn means you have the spirit of a dragon in the form of a human. Here's the thing, what are most dragons like? Most of them want to subdue the mortal races. And Talos was a dragonborn and what is he famous for... really trying not think that the two are related.
This is the TES that turns a lot of per-established TES history on it's head, or at least, made me think what it would be like to live though it. Living in a fantasy world is not all it's cracked up to be.
. Actually, iirc the only questline I actually finished was the mages' guild one, and that one mainly because it's the shortest of the bunch.
