I've made both choices, played two gameplays one for the stormcloaks and one for the empire, my ultimate choice is the stormcloaks. I like to play as it were real life and i was the character, i see the Empire as it were the roman empire and the Nords as the real world Nords, i don't like what the roman empire did to the northern europeans so i sided with the stormcloaks of course, i wouldn't like to see my land being ruled by foreigners, they telling me what i could or could not do, furthermore the Imperial rule is pushing Skyrim back in my opinion they would be so much better by themselves, without the subjugation for the Empire. Actually we should make some considerations about this choice, some argue that the victory of the stormcloaks would weaken the humans in general, since the Imperials would come back and slaughter the Nords with other legions, but i think that if the Nords get free from the Empire they will be able to make their own choices freely, and alliances with the other human races (since the elves have no sympathy for humans, they see the humans as a threat to their lifestyle and such, like the snow elves tried to drive the nords out of Tamriel, and the Ayleds enslaved the humans in Cyrodiil) it's proven in the factions of the upcoming Elder Scrolls Online, with the elves uniting against the human menace. Even the imperials should re-organize their political system, Queen Alessia's dream empire has long vanished and given place to a long corrupt empire, just like the roman empire was in the real world and coundn't stand for itself anymore, it's a matter of time to the Thalmor take over. the Empire including elves and humans is faded to fail, it's a matter of time until the Mers try to get rid of the humans again.
Btw this argument that the Nords are racists is BS, every race in Tamriel is "racist" toward others and they have very good reasons for that, all races have been involved in strifes and wars against each other, and they all dislike and are very suspicious of foreigners, they've learned at cost of much blood that the only way to live in peace is along your own kind, even Nords pro-Empire don't like foreigners in their lands, as BlakBladz said above they want their land to be theirs, they know by personal experience that different races living in the same place will end up in war, it gets time and effort for you to be accepted by the population, if you have played Morrowind you know that, but if you help the people's causes and start doing good actions no matter if you're Khajitt, Argonian or whatever they will start to like you, even more because you're the Dovahkiin, people who are saying that the Nords are racists have no understanding of the TES universe and only played Skyrim because it was cool and hot in the media.
My loyalty is with the Nords and the Humans forever!