Well I don’t see a way to move Order 66 to AOTC but you could add a time jump to ROTS. Or stretch the timespan between Anakins turn + Order 66 and the final duel to maybe a week and make a scene or montage of him fighting some Jedi. The slaughter of the separatist should work as a template, maybe add some lightsabers to some of them and you should be good to go.
Now for the structural change.
The seeds of Rebellion plot line would fit perfectly to bridge the time gap and maybe show how things changed, especially the final scene with Anakin and Padme on opposing sites would be great in this context. (though Palpatine would need a deepfake to get his wrinkly face)
After the senators realized that the won’t achieve anything in the senate, some of them leave with Bail, who made contact with Obi-Wan and Yoda.
The two of them were lead to a small Jedi Temple on some outer rim world, because of a beacon sent by a surviving Jedi. But upon their arrival they find all Jedi to be dead and see a recording of Anakin killing them. Afterwards they change the beacon and contact Organa.
after that they meet up with him on Mustafar where the senators have met in secret. And Palpatine dispatches Vader to sniff out this “rebellion”. But after he arrives he meets Padme and Obi-Wan and the fight ensues.
Something like that should be feasible, what do you think?
By the way, I just realized how stupid the original trap to lure in rouge Jedi was.
I mean sure, ask them to come home and lower their guard after publicly declaring your intention to annihilate them. 10/10, just perfect