I don't think Lucas had an overly complex story to tell in the prequels. I don't think he really had a story to tell in the first place with them. I think his motivation in making them was to hit the reset button on special effects in movie making again like he did in the 70's. The industry had passed so far beyond the things they did in the originals that no one in Hollywood really thought of them as great or even good anymore, just great for their time. The prequels were just an exclamation of "Don't you know who I am !?". So he cobbled together a crappy story to glom all of those visuals onto.
He didn't get someone with actual skill at storytelling to write it for him because he wanted zero constraints of any kind filtering out any of his ideas for visuals. He didn't even let the originals constrain him. The inconsistencies he created within the originals because of this are one of those minor things that really annoyed me more than it should have. Things like Ben telling Luke he hadn't gone by the name Obi-Wan since before he was born.