I always was torn on the choice and never really picked a side in my first playthroughs, instead forcing them into peace through the dragonborn questline. Coming back to it years later though, and having explored the world and the lore, I think I side more with the stormcloaks, albeit very tentatively.
The Empire is a shadow of its former glory and it will never rebel against the Thalmor at the current rate. The empire is simply being bent over and is appeasing the Thalmor to cling to peace a little longer. The idea of a united empire being best to fight them back is true, but sadly, it isn't there in the first place. Half want to fight them but are impeded, the other half do not want to fight at all. United, they are not. Instead skyrim is being dictated at from an empire that really has sold them out.The stormcloak's resentment and anger over it are very understandable.
I do understand the idea of those in the empire trying to keep it together and I can even agree there, but the root is too far past saving without radical treatment, and that treatment will not come from within. The Emperor seems more interested in saving his own skin, so any solution would likely have to deal with him and, well, that isn't going to be any less dramatic than skyrim rebelling.
Now the patriotic Nords are assholes, racist and isolationist. Though most seemed to be decent enough folk, tolerant of those who worked hard and earned their keep. Granted, leadership being racist jerks would cause trouble, though Ulfric, for all his appearances, doesn't seem as racist as first glance suggests. Yes there are slums and segregation, and that is indeed bad, but I recall that lore said that existed before him, and that his own actions lessened the segregation and actively improved the living conditions.
Both sides have good arguments and both are full of assholes. I guess I just see the stormcloaks as the more reasonable choice in terms of what the sides are trying to do and what they might be able to do.