The Prequel Trilogy, of course, is a whole other story.
There are some pieces that conflict when bumped up against the Original Trilogy, but as a trilogy itself, the Prequels work, and it’s clear George Lucas knew what he wanted going in.
For better or worse, George Lucas had complete and absolute control.
He handled all aspects of creating the trilogy and while the Prequel Trilogy is certainly not without issues, a coherent throughline in the plot is not one of them.