I also haven't played Skyrim enough to know...is it really that clear-cut that Ulfric is the good guy?
I think it is intended to be a difficult decision -- shades of gray. One aspect of that is that Ulfric isn't fighting directly against the Elves. He's really fighting against the Empire, of which Skyrim was previously a part, because the Empire's position is "hey, we fought the elves and lost, and this imperfect peace is the best we can do for now." In other words, he's rebelling against the Empire because it tolerates the Thalmor domination.
I'm with Ulfric on that too, though. There are some others who have actually fought successfully against the Elven Thalmor, so what is needed is more guts and less tolerance. Fun game, and the graphics in the north are really quite beautiful.