What the story is about? Well, on the surface, the film's plot is about saving the planet of Naboo from occupation. Overarchingly, though, it details to us how Palpatine came into power and how our three main leads -- Anakin, Obi-Wan, and Padmé -- met. It's similar to ANH in that regard, although quite different as well in that Qui-Gon has a larger focus than Ben Kenobi. I don't find Padmé's behavior odd, to be honest. She's mature for her age and has worked as the head of a largely peaceful planet with many advisors but she is naive -- and the film points this out not only by having her fall into Sidious' trap, but having Sidious himself remark upon it. I would say, too, that the fact that Palpatine is her Senator is also a bonus point in his favor since Padmé is shown to be quite dependent on advisors as well. Likewise, I don't see any issue with the Neimoidians -- there are plenty of people with powerful armies or corporations who are complete cowards. My point earlier, though, was simply to say that I don't see anything wrong with pointing out that RLM doesn't understand the film's story. He himself says this is so.