Are we talking about the primary focus of Episode III pertaining to Anakin or the plot? Because, I thought the ideas expressed in the film, whether you agree or not, were pretty clear, from the Anakin arc.
And the reason Prequel "defenders" don't discuss positive aspects of the films (especially here) is because the debate is framed by Original Trilogy fans...which always veer toward the "suppose" negatives of the Prequels.
And CO, your point about the Prequels having the macro story being Anakin's is technically wrong. If you divorce yourself away from the Original Trilogy and see how the Prequels are structured, the macro story isn't Anakin.
The opening crawl to Episode I don't announce that this film is the story of how Anakin became Darth Vader. Like Episode IV, we are introduced to a conflict. We have our heroes and villians in the conflict. And like Episode IV, the story goes off on a tangent where we meet a character who ends up thrust into the events of the main conflict. Throughout the next two films, like the Original Trilogy, we follow this character. But even then, he's still the micro story.
The difference between now and then is the Original Trilogy. You take any person who has no knowledge of Star Wars and sit them down and show Episode I first, they won't think that this is the story of Anakin....and it will be the same as they go through the rest of the Prequels. It's a story of two conflicts (The Blockade of Naboo in Episode I and The Separatist vs The Republic of Episode II) with three characters (Anakin, Obi-Wan, and Padme) as our anchors to the end result.