Qui Gon was supposed to introduce the Whills to Yoda and Obi Wan in Revenge of the Sith. To Teach them how they can retain their physical form as well as their indenitity in the force, While Qui Gon was just a dissembodied ghost.

I mean it probably was another Lucas idea that got left aside to explain why ben kenobi dissapears in a new hope, and why when qui gon is burned on the pyre in episode one or when he is struck down by maul he remains. But in Return of the Jedi Vaders suit remains on the pyre but his soul and body are gone.

Lucas basically wanted to retell the "Fall of the Roman Empire" in outer space. How a democracy becomes an Empire. While also making reference to hitler and nazi germany. Hitler was chancellor and given emergency powers, before he assumed ultimate control of the country as dictator.

He also blended the themes of Sophocles Oedipus, The story of faust, and milton's paradise lost.

Also drawing parrelells to modern world events and politics. I believe there is an applicability there rather than an allegory of the times of george bush JR.