Personally, my “prequels as 2 movies with Obi-Wan as Episode III” plan involves removing AOTC almost completely, with TPM now being the start of the Clone Wars.

The Trade Federation would be renamed “the Separatists”, and a couple Dooku scenes from AOTC would be added to establish him as the Separatist leader. The end of TPM would feature Palpatine commissioning a clone army as his first act in office, Dooku meeting with Palpatine and saying “war has begun”, and Republic leaders watching the clones be deployed for the first time.

ROTS’s opening crawl would describe the broad strokes of what’s happened in the 14 years since TPM, including Anakin falling in love with Padmé. Other than that, ROTS would be mostly unchanged, just with the standard fanedit trims.