MF points out what I thought everybody realized in his edit. The entire subplot of Dooku as Palp's Apprentice (and therefore a sith) was entirely woven out. Not just the yellow lightsaber and final scene on Coruscant, but also the dialogue between Jango and Obi-Wan. He did a very careful job with this. What I was getting at was an alternate take (based on a really missed opportunity on Lucas' part) where the Sith relationship would be revealed, perhaps in Episode III (where it will inevitably be revealed) and have Dooku with a purple saber instead of Mace. The purple would have been derived from using one blue crystal and one red crystal, if you know your lore on Lightsaber construction. Having Mace with purple denotes him having more of a Sith connection, which isn't who the character is.

As MF's edit stands, there is absolutely nothing wrong with the yellow saber. It works because he did a top-notch editing job on the plot points surrounding the color change.