To be completely honest, both are just as bad, yet just as good.
The Empire is weakened, it is no longer the Empire it used to be, it is corrupt, run by people with greed in their hearts, yet some would say for the Empire 'United we stand, divided we fall'. They want to reunite the continents and bring peace once more.
The Stormcloaks are considered to be racist brutes and their leader only caring for his own goals, yet the Empire betrayed and used him and all who support him, banned the worship of Talos which is what the Empire is all about, seeing their Sons and Daughters being tortured and killed by the Thalmor while the Empire does nothing... A weakened Empire does not deserve to rule over Skyrim.
At first i went with the Empire, but after
Spoiler you capture the Rift, they make Maven Black-Briar the Jarl
and
Spoiler the Emperor is assassinated by you if you join the Dark Brotherhood, and the one who ordered this is doing it for his own gain.
It goes to show how corrupted and weakened the Empire truly is now. Ulfric may seem racist due to the Dunmer in the Grey Quarters, but what Niranye says about them is true... They are too proud of themselves. Ufric cannot care for them while he has a war to plan and people out to kill him. Also, what king has not been ruthless in some ways? They say Ulfric only cares about Ulfric, well of course he has to care about himself, Talos was probably the same, there is no King that is and has been pure, and if they really were racist, the Dunmer would not even be in Windhelm, the same goes for Niranye. His speech when you enter the Palace of Kings is just.