Personally I don't like the Stormcloaks, they're very intolerant (Galmar is a thug who is itching to kill Baalgruf, Ulfric is more reasonable) and I don't think the murder of Toryyg was justified, though the Markarth Incident wasn't fair either.
Now, I'm not insanely thrilled with the Empire either, as the very word "Empire" has negative connotations, but they seem more reasonable and fair, overall. Many Nords support being in the Empire as well. (My current character is a Nord)
I would prefer to pick no sides frankly, if this were all real, but then I'm not playing the full game and getting my money's worth if I don't.
So this play through, after I whack Alduin, I'll join the Imperials.
However, at some point in another play through, I'll join the Stormcloaks just to see those quests.
Just ignore the Civil War thing then. I do most of the time. It's not like it's a very important or even have extensive questline. The way I look at it is that Skryim is so huge and there's so much going on, why would I care if 2 political factions have issues with each other. It makes no appreciable differance in my character's life. Besides, soldiers don't make any money. That's why I came to Skyrim - for money & power. I'm way too old to be idealistic, especially on a fool's errand.
Well, like I said, I want to see everything in the game, eventually.
I'm also looking forward to the next play-through, I'm going to buy and install all the DLCs for that. I know I could run a 2nd and 3rd playthrough simultaneously with the first, but I want to start the game fresh when I add the DLCs (Dragonborn, Dawnbreaker, and even Hearthfire), so I'd rather pretty much wrap up the 1st playthrough, in case it adds weirdness or glitches.
I'm already better than halfway through the game, so.. oh, and then there's the world of mods to look forward to.
The thing I keep wondering about.. I'm deliberately stalling on the main quest, (I'm on The Fallen) so, for now, the truce I brokered is indefinite I guess.. or does the game count so many days or weeks and then say, okay, time's up, ready or not let the war continue?