- Make Qui-Gon Obi-Wan’s elder brother.
- In the Naboo saber fight, Maul cuts off Qui-Gon’s arm. Right before Maul can finish Qui-Gon, Obi-Wan uses a mind trick to sneak up on Maul and kill him.
- Qui-Gon takes the role of Count Dooku. He escapes the Republic, leads the Separatists, yada yada. The key difference is that he is not in league with Sidious.
- Anakin slays Qui-Gon instead of Dooku at the start of ROTS.
Basically make it so that the character of Dooku does not exist and his role gets transferred to Qui-Gon, the Secessionist Light Side Templar.