I personally would like to see the inclusion or even mention of Dooku in The Phantom Menance to better connect Episode I and Episode II. I believe this would really help sell his history with Qui Gon Jinn and make a larger impact on Attack of the Clones when we see he has left the Jedi Order and is working in opposition of the Republic.

Perhaps digitally add him to the council scenes (does not need to talk) or even have him look on as an attendant at Qui Gon’s funeral. It latter could also be a subtle hint at him be Maul’s successor as apprentice to Palpatine and the camera could now linger on both Dooku and Palpatine during Yoda and Mace Windu’s discussion at the end about who was killed, master or apprentice.