I've really quite enjoyed this fanfic. It's clear you put a lot of effort into structuring the plot and pacing it properly so that the story arcs are related to each other and flow into each other nicely. It's that kind of cohesiveness that really makes this whole fanfic worth reading (and now rereading) for me.
I only have a few sparse, and relatively minor, criticisms. Sometimes it feels a bit much when you have randos competing with Tailed Beasts. Like the Four Heavenly Kings attacking the TBs at Kiyomi'Kiyomi's mansion. I get that they were augmented someone, but it somewhat stretches my ability to accept that a substance could exist in the Naruto world that brings people's chakra to the level of a Tailed Beast's. Even with the Akatsuki, they were able to compete for reasons that made sense within the world's rules: Kismet could absorb tons of chakra with Samehada, Hidan was immortal & could cast that curse jutsu, Itachi had the Mangekyo, Nagato had the Rinnegan, etc. And to be fair, I realize that unless someone can put pressure on the powerhouse characters, the fighting would be boring, so I'm not sure if there's a great solution to this. Occasionally I can accept when such characters appear, as Black Zetsu (I'm assuming he is this "Favored Son" character) is just the sort of character who would know how to accomplish this.
Aside from that small wrinkle, I can't help but really dig this story! It's so much more satisfying than Canon Naruto that I can't help but regard it as massive improvement. It makes nearly every character more enjoyable and competent. Naruto, while not exactly a genius, is competent and actually grows as the story progresses. Characters like Sakura, TenTen and Kiba aren't relegated to a worthless status. Lesser characters like Mabui and Samui, in addition to the Jinchuriki Fu & Yugito, are actually fleshed out (not to mentioned, fleshed in, hehe hehe -bloody nose-). And the way you fit in the events of the movies, filler characters and add new characters (like that Priestess Momo) makes it feel like not everything revolves around what's going on in the Elemental Nations.
Keep up the awesome work! The only way I can resist my impatience for new chapters is by rereading the series.