@Robby:
Pulling from the My Hero thread so it doens't get bogged down.
Smart move, I appreciate not having to derail the thread.
I understand your point, especially about One Piece. But I don't necessarily mind having a recurring antagonist faction like the Akatsuki (emphasis on like, it does not have to be them specifically) being the main/final threat in a shonen series. I don't even mind occasionally having some of its members being arc antagonists either. Shonen operates a lot on introducing a brand new villain every arc, but I think that also sort of gets stale in its own right if your series keeps spinning its wheels for years upon years. Feel free to disagree. I mainly stick with One Piece not just to see the next big bad and island, but to see where the plot heading with recurring antagonists like the Blackbeard Pirates, the Marines/World Government, and other characters foreshadowed for years upon years like Doflamingo. Without that sense of progression, One Piece becomes a lot less interesting as a series to binge and analyze since the arcs would then feel a lot more contained and borderline anthological. A type of structure which, although it allows for an amazing range of freedom in creativity, is always going to eventually bore me at some point and make me quit the series for a while if it's long running. I need a consistent hook to keep me invested in a series going for that long that is something other than the main characters just getting stronger. And the later that the final antagonist is introduced, the more risky reader investment is in the protagonist's last conflict being against that person.
And I think that is what's needed to make an antagonist faction like the Akatsuki work in an ideal world where Naruto's concepts were handled better. Progression. Where defeating an Akatsuki member or inhibiting one of their plans has more ramifications than a boss rush mode in a video game, which requires them to be more functional in the overall world events than stealing a new Tailed Beast now and then. Add in the occasional unorthodox antagonist victory, and you have something valuable there that keeps your readers invested in the long haul rather than relying on solely on throwing the next "bigger and badder" fresh face into the mix. Although there does need to be a balance with having other villains along the way instead of just the Akatsuki every single arc to let them not get too repetitive and have free room to breathe as they plan to make new plays. That's what My Hero Academia has been doing with the League of Villains in juxtaposition with the occasional off-tangent antagonist like Overhaul and Gentle, and it's working decently for the most part aside from how most of the characters there still haven't been developed to be interesting characters besides around three people.
The difference between the Akatsuki antagonists like Pilaf, Piccolo, and Vegeta is that an antagonist group like the Akatsuki as a whole is never going to be defeated in one arc. With that many members being so powerful, it's silly. That is an advantage allowing them to stay as interesting long-term antagonists in comparison. The trick is finding out how to keep them interesting instead of doing the same thing over and over again. And there requires a mix of ongoing mysteries, delayed character reveals, character development, different tactics/phases in achieving their goals, not losing all of the time, maybe having the minions be more than just minions and moreso "equal" bosses running independent operations like the Warlords/Yonko but connected to a shared goal, etc. Again, like the League of Villains in My Hero Academia. Although they also have the benefit of not already being top dogs like the Akatsuki and recruiting new members as the story progresses, so the grow at around the same rate the heroes do to give the heroes viable explanations for defeating them while upping their competence so we still take them seriously.
Now, Horikoshi can obviously screw up with the League of Villains at any time. But so far, I really appreciate the breath of fresh air My Hero Academia has in not having a repetitive brand new villain of the arc structure like Dragon Ball and One Piece. It fittingly feels like a superhero comic, but without making the villains repetitive losers who inexplicably keep escaping from jail all of the time in a perpetual cycle because of demand for familiar antagonists.
But making that work for a series like Naruto or My Hero Academia requires a LOT of planning ahead. Otherwise you get another Naraku who is permanently omnipresent, like you said, but has such little progression in stakes and actions that he ends up feeling more like a constant loose end burden than a villain makes you stay engaged with constant suspense throughout the story. Which Kishimoto was clearly never interested in. He winged plenty of Part I if you scrutinize the pacing:
First mission that ends up being the highest ranked mission
Chunin Exams with a full main cast out of nowhere
Village invasion war right that cancels the exams
Training arc with new Hokage search
Rescue arc about Naruto risking tooth and nail saving someone he wasn't even active teammates with for half the series at that point.
Almost every arc keeps dialing things up to 11 instead of allowing time for the series to breathe, set up world building that could actually pay off down the road instead of being sideshow lore, organically introducing new main characters gradually, and dedicating enough time to character relationships so that big events involving them feel properly captivating. Kishimoto just got REALLY lucky because Part 1 had a small amount of arcs that happened to be very long and he didn't immediately hit a ceiling of plot threads/supporting characters/antagonists he was expected to stay dedicated to. But that finally caught up with him in Part II, where you see all the seams fall apart and how much he only cares about main characters that are named Kakashi, Shikamaru, and Guy outside of the cornerstone that is Naruto and Sasuke. And that's not even getting into how much arbitrary plot focus the Uchiha get out of every faction in the ninja world.
I mainly agree with you overall, but I blame Part II's failings more on Kishimoto not properly investing time into planning out his main story beats in the future yet still trapping himself with so many supporting characters and recurring antagonists. Not so much that a concept of an overarching antagonist group like the Akatsuki can't ever work. I don't mind the same plot threads seemingly running forever and ever (One Piece is a testament to that) as long as you keep it feeling interesting and feel like it keeps gradually getting bigger rather than the same goal in sight from start to finish.
Naruto having multiple timeskips like Dragon Ball COULD feasibly work, that idea sounds interesting. I'm just not too keen on everything single "era" being this completely new black slate that can't carry on any old plot threads. They should work as individual stories with their own beginning/middle/end, sure, but they should still feel like they're building up a few things over time if the series wants to keep my interest. Dragon Ball got away with having completely new villains/goals without any overarching story lines for each saga, but I don't really need that again. Especially when series like One Piece and My Hero Academia are showing how fun it is to have recurring antagonists grow over time in balance with new premises/antagonists in-between.