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.