Yeah, that's why I now see Clone Wars as really two continuities (neither really film canon), that both kind of lead into ROTS but in different ways. One is the books and comics published mainly around 2003-2005, the other is the cartoons. They mainly differ in their portrayal of Anakin, and the chronology of his knighthood, scar etc. There's also other cosmetic issues such as the Jedi wearing armor, when the Clones got the new armor etc.
I generally liked the earlier comics and novels for their somewhat grittier takes on the war, and the fact they didn't all boil down to Jedi/Clones vs. Droids. Perhaps because they were going mainly for a fan audience instead of a general audience like the cartoons.
Doctor Who has sort of a similar approach, the original tie-in novels were mainly made for the fans and could get away with a lot more. However when the new series debuted the novels were toned down a great deal.