It is layering. A interesting story for children and also an interesting story for adults. Children see only the glorious Jedi and adults see the cracks and flaws and how the Jedi fail Anakin which leads to his fall. Children seen someone giving in to anger and hate and turning bad. A very good moral lesson. Adults see lopsided teachings, an evil mentor grooming Anakin for an evil future, and a dogmatic religious order out of step with the times. Kids see a story about what not to do and Adults see a story about what not to do - both aimed at their age group. Brilliant story telling. If only the dialog and directing was so brilliant.
George Lucas has said over and over that the films are made specifically for 12 year olds. Over and over. Why would he incorporate something that’s apparently so essential for the story that would go over their heads? Especially when 12 year olds are supposed to be the main audience? He literally says that the optimal age to watch Star Wars is when your 12. How does it make any sense that essential parts of his films would not be able to be digested by children? Because the answer is that it’s not. That’s something you made up. Why would he make the films so that Yoda is obviously meant to be the all-wise mentor figure and the Jedi the good guys? Because he wants children to use the Jedi as a moral basis. He wants children to learn Jedi teachings, AKA his own philosophy.
Also Palpatine grooming Anakin is so obvious children would be able to see it. That’s not something only an adult would be able to see. That’s why you will see adults complain how about obvious Palpatine’s manipulation is. “Why is Anakin so stupid, why can’t he see he’s being manipulated?”, “Why’s Palpatine so obviously evil?” The answer is he’s making it obvious so that children can pick up on it.
The reason people project these alternative meanings on the prequels is because they’re films for children, and therefore will make it more complex then it actually is in a desperate attempt to make the films appeal to them more. Not that the prequels aren’t complex, but the fact is, “The Jedi are good, the Sith are bad” is a still a bit too black and white for some adults. So they have to make it “You see, Jedi ideology is actually somewhat wrong, they say you can’t ever be afraid or attached to anybody, what assholes!” when that’s not what Jedi ideology is. But people wanna cling on because the idea that the Jedi are morally perfect is boring to them. Adults project flaws onto the Jedi because they can’t relate to morally perfect characters like children can.
Um… have you watched the prequels? Us old farts knew Senator Palpatine was Darth Sideous when we saw him in his first scene. Young kids had no idea. The entire PT is written that way. And there is much more. Or else why as adults do we still love these films. His story telling is genius because it has layers for every audience. A five year old can watch it and love the gadgets and ships. A ten year old can love it because the story is incredible. An adult can love it because the story rings so true at every level.
And frankly I think that you ignoring what is clearly in the films is ignoring some of Lucas’s brilliance as a storyteller.
Also, you seem to think that Filoni made Clone Wars and Rebels in a vacuum away from Lucas. Lucas approved every episode of Clone Wars. They worked together, with Filoni learning both about the Jedi and about film making from Lucas constantly for nearly a decade. So when Filoni describes Qui-gon’s role and the deeper meaning to the PT, things that are covered the PT and Clone Wars, I don’t think you can blanket state that the publicaly available comments Lucas has made override that level of apprenticeship that Filoni has had. Lucas’s other public statements regarding things like when he came up with the PT story, how far back Leia was Luke’s sister, etc. are full of easily disproven information so I don’t tend to take Lucas at his word in interviews. He is selling Star Wars and there is a reason behind everything he says, but it is not always accurate to what he was thinking when he wrote the story or the scripts or directed the film. Often he greatly simplifies what he says and makes it sound like that is the way it has always been.
So yeah, when I rewatch that interview with Filoni I don’t hear him explaining what he thinks the PT story is. I hear him relaying to us what he learned from Lucas. His explanation of Duel of the Fates fits the name of the track, the name of the DVD menu title, and what we see on screen. Qui-gon is determined to train Anakin and instead he gets Obi-wan. Instead of a seasoned Master he gets a newbie Knight. Filoni’s interview puts it in words, but his words really ring true. Especially in light of how Qui-gon might have returned in ROTS. But after TPM, it is tracked where Anakin is facing a turning point. I think it is clear from how the track was used throughout the PT that the fate in question is Anakin’s and from there the entire galaxy. Anakin’s fall plunges the galaxy into decades of suffering. And it hinges on that duel on Naboo. It turned on who lived and who died. So I see no reason to not take Filoni’s desription as 100% accurate. He has always been more literal and forthcoming in interviews where Lucas seems to be forever altering things.