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.