Lets face it, both sides of the civil war are not perfect by any means. The stormcloaks in general are fairly racist and do not really want non-nords in skyrim. Argonian dock workers are not allowed inside the city, the dark elves are limited to living in the slums of the grey quarter, attacks on non-nord groups by bandits go unpunished, and the Stormcloak's attacks on Whiterun was pretty much unprovoked. The entire rebellion itself of questionable, considering the threat of the Aldmeri Dominion. They are pretty much playing right into the hands of the elves they hate so much.
The empire isnt that great either. Aside from various examples of corruption and laziness ("Forget the list, he goes to the block."), they have given the Thalmor free reign to enforce the ban on Talos, which they have to know includes imprisonment, torture and execution. It not really surprising the Nords have started to rebel, their former enemies are allowed to roam free to do as they see fit. And while the orcs generally favor the empire, they have simply stood by and allowed Orsinium to be sacked without consequence.
IMO, the Empire is the better of the two choices because of the long term, but really, they both svck. I wouldnt be too happy with them if they were going behead me for no real reason either.