My reasoning for the PT being Imperial propaganda is that the Jedi are shown as superpowered characters who do not care for the common people. Example: In TPM Qui-gon is willing to use Anakin without freeing him, he only seems really interested in Ani after he finds out that he is the chosen one. Obi-wan refers to him as "another pathetic lifeform". Also the Jedi do not allow him to go find or free his mother and they do not allow him to fall in love. So here they are depriving him of his humanity and feeling contemptous of "normal" people. Anakin is the only one who understands what it means to be human(Used in the broad sense not the speicial sense).
We know that Palpantine will become the evil emperor, but if we were galactic citezens we would not know that, we would also not know that he is Sideous. So by showing him as the strong commpassionate leader, determined to restore the Republic to its former glory, but opposed by greedy senators and corperations. He is portrayed as the peoples champion and Anakin is his strong right hand.
The clone wars as portrayed by HTTE,DFR,LC shows a galaxy intent on ripping itself apart different aliens trying to kill each other with clones, some of the Jedi go mad lots of the clones go mad. Humans are united by Palpatine and the empire is formed, the Imerator-class vessels rip through all opponents nothing can stop them. Elite stormtroopers quickly subjagate worlds in the name of the emperor the conquerors(humans) create rules that make aliens third and fourth class citezens.
Republic->Clone Wars->Darktimes(clone madness)->Empire.
The other way as shown in the movies: Greedy corperations backed by cloaked warriors/manipulators, trying to oppress the peoples. These corperations are well equiped with powerfull weapons even by OT standards. It is an uphill fight for the valient forces of "good" trying to bring peace and justice to the galaxy, while being opposed by not just greedy corps. but also by greedy republic members and their backers the jedi not wanting to lose their elite status also try and stop the "good guys".
Having said this I am feeling better about the movies because I just saw the trailer for Ep.III, and they have Juggernauts which are EU. Which makes me happy.
At a guess he's refering to one line in the TTT where they mention 'clone masters' unleashing clones on the galaxy hence; The Clone War.
Personally that's the image I had in my mind too from Obi-Wan's spiel in ANH about the Clone wars.
Same for me I just thought about it to much and it upset me.