Moving this idea over from the Animated Star Wars thread, I must confess the idea of either Dooku replacing Qui-Gon or Qui-Gon replacing Dooku as the Seperatist leader is one I really like.

I don't know how it could be done but it makes so much sense that the Qui-Gon would be the father of the Seperatist movement and the Rebellion (I wouldn't like him being a Sith Lord though).

After the success of the Clone Troopers in Episode Two it would make sense for the Seperatists to get their own clone troops or (going by Grevious) cyborg troops.