Because I have been extremely disappointed with the Eps I-III, I decided to write my own canon. But also have been recently exposed to some of the EU I am open to that as well. But the main story needs serious revision in it's early stages in my opinion.
The origin of Anakin - crap!!!
The the additional information about the force in Eps I - III, crap!
The seduction of Anakin - crap!!! (the whole story of Anakin before Vader is all major crap IMHO).
Most of the Jedi being wasted by Clones - big huge turd.
The fact that Vader did not hunt down the Jedi and become more "Vader" through limb loss and battle scares in exterminating the Jedi - total hairy and runny crap!!!!
I have other revisions in my head, but that list hits my major discrepancies with what Lucas did with the story. In early interviews he told a different story (in the details) from the ones he eventually put to film. Shame, what he hinted sounded a lot better, or I just completely misunderstood him as a kid. But most of my revisions are based on what I believe he alluded to in interviews.
There has been some good stuff in the CW cartoons, but again anything pertaining to the force and how Lucas has flushed that out is garbage in my mind.