Honestly. I see nothing good with joining them, but then again, I am a Stormcloak at heart. Some Stormcloaks are racist, yes, but that can be worked out. A broken and corrupt Empire cannot be fixed.

I'll answer for most.
Nostalgia
Nord hate
Romans

Most people have their reasons (They will list them and another civil war on the forums might start).

As for me, I don't side with either of them, why? because the real enemy are the Thalmor.

I see the Roman Empire when I look at the Imperials... I don't reallt see much in the Stormcloaks...

Also, I dont want no Dominion takin' ova mah homestead

Then fight for the Stormcloaks. At least we rid Skyrim of all the justiciars after we win the Civil War. Unlike the Imperials who continue to bend over with Tullius' vague promise of a backlash.

Tullius tells Elwen to basically shut the [censored] up in the peace meeting, and hates the thalmor as much as the stormcloaks (He even frees a stormcloak prisoner if you ask him and your in the legion.) So dont compare Tullius to that.

One word, Romans.

Hmm, never thought about Thorald. Last time I asked Tullius about freeing him, I wasn't in the Legion. Tullius is a good man, though.

A minor bug prevents the option, but if you get the pc patch, it fixes it.

Also, Hadaver risking his life to save a little child from Alduin gave me a postive impression for the legion in Helgen.

Ah, well I always join the Stormcloaks and I always enjoy slaughtering every Thalmor in that keep anyway so I don't need to ask Tullius to release him. I release him myself, with a lot of bloodshed.

Regarding Hadvar. With your logic, we could also say the Legion gave one a negative impression when trying to behead you.

Well, on the face of it, the Imperial Legion does stand for a position that seems very reasonable. Stand united while you rebuild, and don't let the Dominion split us apart. And the Empire-supporters in-game are very quick to denounce Ulfric for opposing this position. And people like Rikke and Legate Fasendil are, I think, meant to be genuinely good people, with the heart in the right place, which is rarely questioned. The Empire is also, unfairly I think, given a presentation of having the "racial equality" thing on their side, which is an emotional heavy-hitter for many, since racism is something I think many people have had to deal with themselves.

On the other hand, the Stormcloaks appear very pro-Nord, which is easily twisted to mean anti-non-Nords, and they are constantly being berated for endangering a peace that cost the Empire a great deal. And the leaders of the Stormcloaks are more questionable than the people who are perceived as the leaders of the Empire's position*. Rikke and Tullius seem to be pretty good people in general, while Ulfric has a complicated past that require a lot more research and evaluation of evidence. Galmar, while seeming like a good enough guy, is very blunt and unapologetic about his position as well, which can be off-putting for some people.

A misconception of the state of the Empire is also a possible, though I think a lot less likely, of a reason some might have. Back in Oblivion, and to some degree in Morrowind, the Empire was a strong force that appeared very rosy. They were almost always put in the position of good guys. Especially in Oblivion, where the last Septim is an incredibly selfless man that was willing to give his life to save everyone else.

Compare this time of the Empire to a time when the Empire is all but falling apart, even though the information about what has happened for the Empire in the last 200 years isn't nearly as accessible as taking a look at Oblivion, which is set in the province of Cyrodiil, the heart of the Empire. I don't think most people know that not that long ago cities in Cyrodiil erupted in gang violence or fell to an unspecified force, or that under the Empire's protection the kingdom capital of Wayrest was sacked by Corsairs. I also don't think most people have read the Brief History of the Empire, which portrays the Empire in a far less bright light than the games. Same with books like Eastern Provinces.

And when there is conflicting information, a lot of people will just side with the people they personally like the most, and since Tullius and Rikke don't have NPCs going around badmouthing them all the time, they are much easier to think of as likable.

If it wasn't for the 200+ years of decline and the death of the Emperor at the behest of a member of the Elder Council, I think there would be a fair case to make for the Empire. At least on the grounds of longterm planning against the Dominion.

Also, I don't think it does the Stormcloaks any favors that the Nords are white humans, given humanity's recent history. I think a lot of the charges against the Stormcloaks would die down very quickly if it was a Redguard movement, because of western societal perceptions.

Another interesting observation would be a few polls made, regarding people's favorite race and who'd they'd support in an alternative civil war on as close premises as possible. I think a lot of people just can't identify with the Stormcloaks' cause, or don't care, so they'll support the other side.

http://www.gamesas.com/topic/1471531-if-the-situation-was-different-v11/

http://www.gamesas.com/topic/1458239-if-the-situation-was-changed/

http://www.gamesas.com/topic/1472866-insert-rebelling-race-here-vs-empire/

I don't think these polls necessarily are absolute, as the number of people who voted is too low, but since the same trend occurred in all three, I do think there is grounds for saying that the Empire tends to get support because it is the Nords who are rebelling, and not the favorite race of their own rebelling. I also think you see some of this in the fact that many of the Stormcloak supporters tend to like the Nords in general.

Edit:

*Which is very deceptive by itself, since the actual leaders of the Empire never appear for long in the game. The only real leaders of the Empire you meet is a fairly likable Emperor... and the shady guy who has him killed. And, even so, given their minor role, I don't think people perceive them as the leaders of the Empire. Also, it is very easy to buy Motierres "we have to kill him for the greater good"-story, since it appeals to the already put-in-place "Greater good" narrative the Empire plays on in this conflict.