I joined up with the Stormcloaks in my first playthrough and regretted it so much I re-started. After playing for a week. I'll explain my reasoning for anyone who wants to read it.
I don't like Ulfric. Never did. My plan, as the Dragonborn, was always to support the Stormcloaks and help them take control of Skyrim, then kill Ulfric and take his throne. I'd already be the saviour of Skyrim at this point. Alduin's bane. Who'd oppose me? Who could oppose me? Who'd dare oppose me?
I would now be High King of an independent Skyrim, full of peasants who love me and nobles who either love me, or obey me out of fear, for I'd be a legend who'd stepped out of the stories of their childhoods.
The only land routes into Skyrim are narrow mountain passes, easily defendable while I rebuild the country. It has just struck me in the last five minutes that Skyrim's north coast is just that - a coast. The Stormcloaks probably don't have a navy. The Thalmor certainly do. I suppose I might capture whatever fragment of the Imperial Navy's ships that were berthed in Solitude, and I would have their ship building facilities as well. If the Thalmor did attack, they would have to land on the rocky, stormy coast, and face off against an army of furious Nords who are very adept at fighting in brutal winter conditions. And me, don't forget me, who can burn their ships with a word, or hurl them off mountainsides, or cause entire companies to flee in unnatural panic. With skill, and a little luck, I could harm the Dominion terribly without having to leave home.
Obviously my plan from here is to lead an army out of Skyrim and re-found the Emipre, Tiber Septim style.
Here's why I regretted joining the Stormcloaks:
I could probably accomplish the same thing with the Imperial Legion. It might require a bit more subtltity than "Eat this sword, Ulfric", but I could do it. I could put down the Stormcloaks with the help of General Tulius, gain his confidence, become a dragon-slaying hero, marry the widowed High Queen and perhaps even demand the Dragon Throne by right of blood if not right of might. If they say no, I could probably stage a military coup, Tulius might even join in, he seems to be mostly autonomus in Skyrim, answerable only to nobles hundreds of miles away. If I did break away from the Empire like this, I could also reinstate Talos worship, winning over many of the former Stormcloaks as well.
I don't care that you can't do any of this in the game, it's happening in my mind!
Anyway, what do you think? And yes, I have been reading my Macheveili...