I'll agree that the dialogue is poorly written by Lucas, but the motivations behind the characters are clear based on the actions each takes, and the story itself is great.
He had the same problem with Jar Jar in TPM. The character is supposed to be grating and annoying to the characters around him. That's the point. Yet Qui Gon believes Jar Jar is worthy of compassion and life regardless of those flaws. Eventually Padame sees this as well and it helps save her people. The problem is that Lucas made the character grating and annoying to the audience to the point that it messes with the story.
Same with Anakin and Padme. Anakin has been obsessing about her for a decade, has no experience in courting, and also has a massive ego due to his abilities with the force. He's not supposed to be a suave ladies man who sweeps Padme off her feet (ie the infamous 'sand' conversation).
Padme starts off flattered by the attention of a Jedi, then pushes him away when she realizes how serious he is about her and that he doesn't just want a fling while they're on a adventure together, then pulls him back close after his confession about the sand people in the misguided hope that it will 'save' him from his darkness (and also to comfort him in the face of imminent death). In some ways, she's applying the same lesson she learned in TPM with Jar Jar to Anakin, but it doesn't work because the secrecy and deception distorts it, and only becomes worse when she becomes pregnant in RotS. Meanwhile Anakin's hero complex (again, started in TPM when he wins the podrace and helps win the battle of Naboo, and was shown growing over his apprenticeship with Obi Wan via their dialogue at the start of AotC) and unhealthy obsession with Padme (like, the first half of AotC he is very, very stalkery) join together in RotS into tragic consequences.
In RotJ, Vader's love for his son saves Luke, but in the Prequel's Anakin and Padme's 'love' dooms them both, because the later isn't real love. To me, the story Lucas is telling is clear, even if what he wrote muddles it so bad as to lead to misinterpretation about what's happening between them. Put another way, the text of Lucas's writing is very good, it's the texture that's so off as to mess up the emotions that the audience should be feeling about what's happening when they see it.