I don’t think anyone here is claiming that ROTS communicates all of it’s themes and ideas as well as it should have, the point is that they are there. Lore-wise the PT works quite well, but cinematically it fails on many points.
Exactly. The points are all there for people who watch the films repeatedly. It is not clearly done for the casual observer, though a lot might catch certain things and not question his turn. I think one of the biggest issues of the PT is that is really isn’t a prequel at all, it is a flashback. We already know Anakin becomes Vader so things aren’t setup very well if you follow the story chronologically. But the points are there. Palpatine maneuvers Anakin into an impossible position - save his friend and mentor who just might be able to help Padme or save a revered Jedi master who seems to be trying to take over the Republic. Which one is his duty to the Republic? Which one is the right choice? And as we see, he listens to Palpatine. He killed Dooku on Palpatine’s order. So when Palpatine has Anakin in that vulnerable state, he uses the dark side of the force to pull him the rest of the way over. He goes and slaughters the Jedi to preserve the Republic. It becomes the very thing he joked with Padme in ATOC. In point after subtle point, Lucas reinforced Anakin’s fall.
And it seems clear that Palpatine is the one person Anakin trusts the most. So if Palpatine says something, Anakin will believe it. And he will believe it over the Jedi because of his long acquaintance and friendship with Palpatine. He probably has had more contact with Palpatine than any single Jedi. Palpatine made sure of that.