Sorry for being years late to the party:
Throughout my playing and replaying Skyrim over the past few years, I've played both sides of the coin, but I usually choose the Imperial Legion more often than not, because one, I get better armor and weapons as a Legionnaire versus as a Stormcloak Rebel and two, the Nords are racist as all hell towards Non-Nords, but Legionnaire Nords don't seem to care if you are not a Nord. I happen to like Hadvar, he feels bad that his superior officer pretty much signs your life away even though you are not on the list and are obviously not a Stormcloak Rebel. Hadvar even apologizes and mentions making sure your remains (if you were executed) are returned to your homeland. Ralof seems to care less about you and vanishes for a bit after telling you to jump into a burning building. Hadvar, on the other hand, tells you to stay close to him if you want to stay alive, meaning that he will do what he can to protect you. After escaping Helgen, if you walk with Hadvar (despite his saying that you should probably split up), he admits that he knew that you shouldn't have been on that cart with the other prisoners. He even tells you that if other Legionnaires encounter the two of you on the way to Riverwood, to allow him to do the talking, pretty much in order to protect you. Ralof, seemed to me to only care about himself and you were merely an afterthought.
I also prefer the Legion due to my dislike of Ulfric. Sure, he was considered a Hero to some and a legend to many, but the fact remains that he murdered the High King, regardless of challenging Torygg to a duel. I scoured Skyrim and learned that Torygg actually admired Ulfric and likely would have been willing to peacefully talk everything out, but Ulfric murdered him to, as Ulfric admits, prove a point to the other Jarls about what happens to those who oppose Ulfric. I personally see Ulfric Stormcloak as being a power-hungry individual who doesn't give a crap about anyone but himself and his rise to power. He literally waves off most concerns that don't directly effect him. He is so busy trying to bully his way to power, that he doesn't really seem to care about anything else going on such as the Dragon Crisis. I went out of my way to speak to many NPCs in Skyrim about their own thoughts of the Civil War, even Ulfric supporters admit that they believed he murdered Toyrgg and that the High King would have been willing to listen to Ulfric, but Ulfric wanted to be High King and was willing to do whatever it took to get there. I admit, his whole speech about wanting to wait for the Moot to appoint him High King was a brilliant move. Ulfric knew that many would still oppose his claim to the throne and his speech made it seem to opposers that he wasn't as power-hungry as the Legion claimed. Remember the first official Civil War quest? Retrieving the Jagged Crown? Ulfric wanted that crown because he believed that possessing it would make the other Jarls more likely to bend to him because he had an ancient symbol of the High King. His decision to keep Elisif as Jarl of Solitude was also a brilliant move, because he knew that not only killing another Jarl was bad for his image, but the fact that she was Torygg's widow would have made the situation worse. If he had killed Elisif, there would have been no doubt, even amongst his supporters, that he was a power-hungry murderer.
Sure, the Empire is not as strong as they once were, after the Oblivion Crisis and the Great War, it's to be expected. I also personally don't like Titus Mede II and I believe that his assassination opened the way for a better, more competent Emperor. Skyrim is only one Province and the Stormcloak Rebels lack in quite a few areas, including manpower and supplies. Maybe if the Stormcloaks were lead by someone else and had better equipment and more manpower, they might, MIGHT be able to face the Dominion. From what I could tell, through my travels around Skyrim, the Empire and the Dominion were actually at a stalemate when Titus Mede agreed to the terms of the treaty to avoid more bloodshed. Afterwards, the events of the Markarth Incident and Ulfric's actions drew the attention of the Dominion. They had, up to that point, largely been ignoring what was going on in Skyrim, but Ulfric decided to make a fuss when the Empire was forced to renege on the deal that Markarth's Karl made with him, which broke the terms of the treaty, and thus, the Thalmor ended up in Skyrim. I think that if Ulfric had quietly admitted defeat, metaphorically, and returned to Windhelm, the Thalmor wouldn't currently be running amok in Skyrim. Ulfric's actions led to Thalmor presence in Skyrim and in his mad dash for power, the people he claims to love and wants to protect are now suffering from the war and the Empire is wasting resources trying to quell the rebellion. Ulfric himself was a Legionnaire Officer, he knew exactly what the consequences of his little rebellion would cause, but he doesn't care. All he wants is to be High King and his repeated actions prove that he is simply power-hungry. He deludes himself into thinking that he would be better High King and that an independent Skyrim could stand against the Dominion. So, what happens if the Dominion becomes larger and more powerful? Skyrim is screwed. As many NPCs say, a united Empire is better for everyone. If the Empire regains its strength and reunites the territories it lost after the Oblivion Crisis and the Great War, they would have a better chance of beating back the Dominion, who only has 3 provinces out of 9 under their control. If the other 6 provinces unite with the Empire, either permanently or temporarily, the Dominion would be outnumbered. However, even an independent Skyrim or Hammerfell fighting against the Dominion is not enough, they are still outnumbered. Ulfric isn't looking at the big picture. He wants only what he wants and what would benefit HIM the most. Therefore, I usually side with the Empire. Also, my current character is an Altmer Battlemage who is a Legate in the Imperial Legion and who openly worships Talos and is an 850 year old Vampire Lord.
Sorry for being so long winded.