I will say that the Darth Plagueis book does a magnificent job of turning the prequels into a coherent setting where almost everything does actually make sense in context, but that’s just the issue, it takes an entire extra book’s worth of context. People that have read that book are going to retroactively imagine details in the movies that were never there and were not explained at all.
I said it before, I will say it again. The Prequels are a really good story if you take the time to explain everything in detail. But three movies are not enough to explain everything that needs to be explained in detail, and the Prequels should have never been movies in the first place. The Prequels should have been either a long, live action TV series (4+ seasons), or an Expanded Universe multimedia project of books, comics and video games that are interconnected to each other, something along the lines of the Clone Wars Multimedia Project that existed in real life, but including the main story of the movies too. The problem is not the story that Lucas was trying to convey to the audience, but rather the fact that the story is not suitable to be portrayed in three movies. The story is way too complex and contains a lot of information. Three movies are not enough.
I think the problem was the story he was trying to convey, or at least the details of the story. The extra details that fleshed it out and made it make sense came later from other people doing their own interpretations, and those extra details didn’t exist at the time. There essentially was an EU multimedia project, just not all at once. But there shouldn’t have to be. It’s a movie series that exists to be watched as movies, and it’s unreasonable (especially in 1999-2005) to expect everyone to invest time, money, and energy into puzzling together your story for you like homework. You have almost 7 full hours of screentime, plus the direct exposition from opening crawls. So much of that is wasted, or in the case of the “taxation of trade routes” thing we’re talking about, actively makes it less clear.
I think that you missed the point of what I was trying to say, though. I didn’t say that you are required to spend money and time reading and experiencing EU stories to fill in the gaps, I said that the Prequels should have been conceived as an integral part of the EU from the very beginning. We shouldn’t have Prequel movies, we should only have Prequel books, comics and video games, and possibly a TV show. This is the only way to preserve the core elements of the story that Lucas was trying to convey, while simultaneously expanding them, exploring the overall setting, locations and characters in detail, and making everything feel more believable. The Original Trilogy is able to stand on its own, because it is a simple adventure, a classical hero’s journey that doesn’t require a very complex world-building. But Anakin’s story from his childhood to his transformation into Darth Vader? The Clone Wars? Palpatine’s rise to power? Nah, these are all things that necessarily require a complex story, a lot of world-building and a lot of explanations, all of which are not feasible for three movies, unless you end up making movies of 6 hours each.