One example that I think demonstrates this perfectly was mentioned in the “Vader is a chump” thread.
The prequels have this prophecy running throughout that Anakin is the one supposed to bring balance to the Force. At the end of Revenge of the Sith, the only Force users left alive are Palpatine (Dark master), Vader (Dark apprentice), Yoda (Light master), and Obi-Wan (Light apprentice). Two sides of the Force, two people on each side. Anakin did truly bring balance to the Force, except it was not at all in the way the Jedi assumed, which is that the Dark Side would be obliterated entirely. It was that naivete and arrogance that caused their downfall.
This is actually a really good plot element. Not original by any means, but it highlights a sophistication in the story and is consistent with occasional hints that the Dark Side isn’t necessarily evil in itself, it’s simply the chaotic, emotional side of the Force, whereas the Light is the orderly, emotionless side. This is a concept that has significant play in modern fiction (just to name two examples, Babylon 5 and Magic: the Gathering, in which White is not necessarily good and Black is not necessarily bad). By itself, it didn’t make the prequels, but I did give Lucas a good bit of credit for it.
…And then Lucas states outright that “bringing balance to the Force” refers to Vader killing the Emperor in Return of the Jedi and destroying the vessels of the Dark Side for good. In one fell swoop, Lucas completely destroyed any sophistication in his story and reduced it to a simplistic “Light = good, Dark = bad” equation. It removes that extra dimensionality the story badly needed and turned it from something potentially interesting into a story you might expect a child to write.
Now, sure, the comment from Lucas isn’t contained in the movies themselves, so I can ignore it and look at the story as the movies present it, but it’s pretty strong evidence that Lucas doesn’t understand his own story and makes poor and confusing decisions. If “bringing balance to the Force” entailed killing Palpatine, why end Revenge of the Sith with exactly two Sith and two Jedi? Why point everything at the balance between Light and Dark if that isn’t actually the idea you were driving at?
Lucas is simply an ineffectual storyteller who got as far as he did through sheer luck. And I really don’t want to hear about how Star Wars has always been for children and so doesn’t need more than a simplistic plot. The best children’s movies are well-rounded and appeal to adults as well as children. Look at anything from Pixar. Science fiction/space opera also need not be childish and silly; Babylon 5 was an exceptional space opera story. Many authors who’ve participated in the Star Wars Expanded Universe have done a wonderful job of creating engaging and interesting Star Wars stories.
Lucas is entitled to whatever story he wants to create. But I don’t think it’s unfair to point out the ways in which it could be better, and it’s frustrating when the improvements could be so trivial.