Meh. On the one side you have the Stormcloaks--insular, some have claimed that they are racist, yadda-yadda. On the other hand, the Imperials, who seem to have no problem executing people without trial if they're in the wrong place at the wrong time, have no problem carrying out orders to execute people even if they seem to question it (opening scene, "By your orders, Captain") and have tried to wipe out the religious beliefs of the Nords, because...well, just because, apparently.
Both sides have a point about the other. To say that the Nords are "racist" strikes me as a little silly. They live in a part of the world where they don't have a lot of contact with folks of the other races, so there's some suspicion, but Ysolda was praising the (I believe) Khajiit that was going to help set her up in business. They don't much like being absorbed into the Empire, but I can't really fault them there. Listening to the people in the street and the loony preacher in Whiterun, the Empire not only wants to absorb their territory, but outlaw their religion. That, understandably enough, makes them a tad cranky.
On the Imperial side, they are, more or less, looking at the big picture. They know that a united land is more likely to survive than a fragmented one. They just seem to be going about it badly in that, instead of uniting the world diplomatically, they're attempting to do so at the point of a sword. They're trying to make too many changes too fast for people to accept. They've got military discipline on their side, if nothing else.
Again, meh. Both sides have good and bad points. What people tend to forget and as the game serves to remind us, there are very few instances of "good guys vs bad guys" in the world. There are, however, a metric boatload of shades of gray. Paraphrasing Shakespeare's Henry V here, but what king ever entered battle with nothing but unspotted men?