It has nothing to do with his supposed "vision." It has everything to do with making three films two decades later and deciding not to do your best to make them fit with a pre-existing trilogy. It's not his overall vision that's different. It's the fact that he did small things in the prequels that conflict with established mythos when they could have easily been changed to avoid this. Instead, he went full kilter without regard on the ideal that, "hey we can always make more changes."
I'm saying that the changes shouldn't have been needed at all, given the clean slate and a pre-established set of creteria to work with.