I've sided with the Stormcloaks just to see what was what (it was my first time playing, and had no idea why they started the civil war to begin with.) I waited until my Khajiit assassin was at least lvl. 20 before traveling to Winterhold to talk to Uflric about joining the rebellion.
It wasn't long before I realized that, at least in my opinion, siding with them was a bad idea. The biggest of the problems (and, evidently, the most common one among gamers) I had with them is they are incredibly racist. Then, there's the Thalmor dossier, where you find out that Ulfric had, in fact, helped them (it's highly likely that, since he helped them, he'll help them again.) And, finally, there's the empire, who would fall under the heels of the Thalmor if Skyrim broke off from it.
Next time I play, I'll start my character over and take the side of the Imperials if I pick a side at all.