I'm not much of a lore guy, but here's my personal opinion: I think the Stormcloaks are the good guys here. The main issue, to me, is the Thalmor. The peace treaty that the Empire signed in order to the end war gave the Thalmor permission to not only skulk freely around Skyrim, but to literally capture and execute Nords simply for practicing their traditional religion. This should sound very, very familiar to real life events (you know, WW II). It's not that the Empire is bad overall--it's that they made a bad choice. Most of the justification for what the Empire did comes in the form of "well, the Empire was between a rock and a hard place, so they signed the peace treaty." In other words, they backed down in my opinion. When it comes to scenarios like this, I'm more of a "win or die trying" type of guy, so I support the Stormcloaks. Also, I've played through both stories and have found Tulius to be a fairly weak, uninspiring man who is just going through the motions. Compared to Ulfric, who is a strong, determined leader driven by passion and a legitimate oath to his people. That's my take. One of my favorite things about Skyrim is that you can really make it your own.