Not sure how it would've worked. Remember at the end of TPM, they ask "which one was it, the master or the apprentice?" Sure, we knew the answer, but in terms of the story, it wouldn't make a whole lot of sense to have that apprentice sticking around 'til the end and removing Dooku altogether - there still had to be some mystery surrounding the Sith because, if you remember, they didn't know who the Sith lord was in EP3 until the very, very end. Just my take.
If I die today, I'm happy how my life turned out