I (and most of the people I've shown TCW to) found Dooku's character change from a lying, manipulative, Sidious subsidiary to a rogue Jedi who has learned the terrible truth of what's really going on in the galaxy and is doing what he thinks is best to correct it, a superior take on the character. Not to mention it eliminates the rather questionable actions on Dooku's part if he was in fact a Sith, such as his conversation with Obi-Wan and his confusion over the Republic Army with the Geonosians. As cool as the ending scene is with Sidious and Tyranus, the plot is far better without it.