Vladius said:

I'm saying it might feel undeserved if there's not enough character development through the scenes in the movie to begin with.

Well, my view is this:

At the end of the day, nothing beats good old fashioned character development and exposition on the screenwriting level....but music can work as a substitute up to a certain point.

Giving Dooku a theme doesn't make up for lack of development in his character, but it does give him more uniqueness and personality which isn't a bad thing no matter how you look at it. If Dooku is the central antagonist of the movie (or a sub-in for one at least), then it makes sense to me to do everything that is possible to strengthen him as a character. Whether or not his character is deserving of an epic John Williams-ish theme is certainly debatable, but at least it would give him something to stand out.