I've always rooted for the bad guys: the Empire, the Decaptacons, Cobra, you name it. Why, you might ask? I would have to say because the villains are the progressive forces (if I may borrow a term from the DU), whereas the good guys represent the status quo. The villains seek to unify the globe and usher in an age of order and peace (which is only possible when 1 figure/civilization is so dominant that all rivals must submit or be crushed), while the heroes fight for factionalism and chaos.
Plus, the bad guys know what they want and they go for it. They rarely succeed (because they are usually inept), but you have to admire their pro-activeness. Good guys, meanwhile, are reactive--they only respond to the villains and never initiate anything on their own.
Not to mention that the bad guys are, as you said, so dang cool.
I remember saying about the first of the new Star Wars films, "Any planet who elects a pre-teen girl to be their galactic queen really, seriously NEEDS a little external guidance."
This made me rethink the entire Star Wars dynamic. The empire was "bad" only because it was stated that they were "bad" in the exposition of the film, but all I saw of them was one cool as anything space station and some pretty decent organizational skills.
Granted, the destruction of Alderaan was a BIT harsh, but it drove a point home.