And though I'd have probably left in the final scene with Dooku and Sidious, showing them in allegiance as the final twist, MF deftly handled weaving out the entire subplot and making his notion of Dooku simply a rogue Jedi totally work.
MF, regarding this idea about Dooku and a purple saber, would that have addressed any of your issues with the red flashes any better? i.e. Would the purple have done more to hide the red than the yellow did? And again, I think the yellow saber with the red halo and flashes actually looked pretty bitchin' on the whole.