I was talking wth my buddy, a SW fan but not die-hard like on these sites, about how I think you could have rearranged the films having seen the CW toons in their entirety and how they fit within the prequal trilogy, and I was surprised (he's generally the kinda guy who likes SW but kind of enjoys picking on me for liking it "too much") he agreed with me.
For me, I'd have gone with this formula...
-AOTC would have been Episode 1... Have Anakin found as a teen, Luke's age or so (draws a stronger parallel IMO and explains Yoda's reluctant desire to train Luke at that age if Ani had proven such a mistake), and have him trained by QGJ and Obi-Wan... QGJ dies by Dooku's hand. Eliminate the Darth Maul character totally or have Sidious toying with two pawn Sith Lord apprentices and do away with "There's only ever 2" crap or have them unaware of each other even.
-Clone Wars takes over as Episode 2... Develope a single story to fill the 3 years of war (or at least portions of that 3 years, and still have cartoons filling these other gaps) that show Anakin's growth and rebellious nature to Obi-Wan, with the war sort of pushing them apart, his love of Padme developing (TPM didnt' do much for it IMO), etc...
-E3 leave it pretty much as-is with the war's end.
If you want, do an animated series that can include the podrace as something Anakin did in his youth that showed his ability... Have Jar Jar's asinine behavior more focused in the toon that sort of replaces TPM... Have it be short stories, not one long continuous one, and not intertwining characters like Obi-Wan, QGJ, and ANakin... Just instead showing their earlier adventures each on their own.
That's just my thinking on it, in a brief format... I think it would have made for a much more powerful Prequal trilogy myself.