My plan for the prequels:
Anakin is much older is Episode 1 and is already being trained by the counsil. Smoothly slide in some bad character traits but only just so.
In Episode II, Anakin turns to the Dark Side and the beginnings of the Empire take shape... but not all at once. Jedi are declared outlaws at the end of the film.
In Episode III, the Empire has been fully approved by the senate, the old republic is crumbling and Darth Vader is hunting down every last Jedi.
I personally think that would have been much cooler.
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