Some ideas relating to the timeline to make it match the OT’s implications a bit more.

TPM takes place years earlier then it does in canon (around 5-10). This has a ripple effect on AOTC, though ROTS has to stay the same.
Gradually we see the Jedi’s numbers decreasing. Empty seats on the council, less of them walking around. Perhaps by ROTS, there’s only a quarter of the council left. Try to make a point of the Jedi getting gradually “kicked out” of the government.
The Clone Wars lasts longer. Anakin becomes Vader in his late 20s rather then early 20s.