The Trade Federation’s role could be reduced. TCW without the prequels implies that the Trade Federation is distinct from Nute Gunray and the other Nemoidians who support the Separatists. Anakin could be the good friend that the OT implied he was.
A number of stupid PT elements would still remain – Darths, younglings, Gungans, Chosen One prophecy, etc.
That doesn’t mean that a TCW-compatible PT would have to reference them. Also, we could be selective as to which TCW episodes we include in the continuity of our rewritten PT.