The OT part in D&D is a little weak. Mostly because they reverted back to the early wacky adventure strips of their version of TPM, whereas the PT part has completely revamped characters and story (probably because the PT are crap).
Maul, Fett, Palpatine, Windu, none of them are like their theatrical versions. The plot twists were brilliant, and many of the concepts of both AotC and RotS are far, far, far better executed in the webcomic than in Lucas' movies. Just to put an example, by the time Windu went to fight against Palpatine I was actually paranoid of *all* characters and their intentions, and while I knew Anakin would eventually fight against Obi-Wan and became Vader, I didn't know how the rest of the story would eventually end. And I love some of the meta-humour (Annie, who had no roleplaying experience, playing Anakin).
By contrast, the OT-exclusive characters (except Chewbacca) are just exagerated versions of themselves (Han is dumber, Luke is cockier, etc). And once Pete's newphew became a regular player all the rich player-to-player interaction and story was scrapped and the movie's adaptation became more straightforward.
It's still funny, there's still brilliant concepts, but overall the best part are up to the end of RotS.