It interests me that, in the modern day, virtually all battle manga which find success in Jump have the protagonists becoming a part of an organization which they act in subordinate to. Gone are series like Dragon Ball and One Piece (which is still running, but whatever) where the protagonists are purely the organizers of their own fates.
Anyone have any speculation on why that might be the case? Especially interesting when series like TPN and Stone do do that?
I think you have used the wrong word here. Neither Gon nor Luffy are an "Organization" they are a band of friends who either happens to always fight the evil that comes along their way or are just on their merry way to become kings of the world and happen to fell into one adventurer after another during it. If you say decider instead of organizer then it would fit both Gon and Luffy as they decide what they do, sometimes even surprising decisions you didn't expected as a reader. An organization on the other hand is far bigger than a couple friends with the same goal in mind, it is a structure of strangers who actually do not necessarily have the same goal in mind but work together nonetheless for their own reasons, usually money for the not main characters though sometimes money is also an issue for them.
A MC building his own organization would mean a huge amount of trouble for a mangaka as not only he had to create a huge cast of characters but actually has to show how the MC could create an organization out of nothing. It is far easier to have an already established organization and have the MC and friends join it and then later explain it one by one.
If you look at KnY, BnHA, CSM, AA, WT, UU and so on you do notice that the MCs often do make decisions regarding their own fate, often against the orders/wishes of their superiors. However those MCs do need the organization for more mundane but really important stuff. You need apartments to live in, food to eat, weapons to fight, medicine to heal, information to gather and a MC usually cannot do that all on his own. In DragonBall most of that stuff simply ain't important you can sleep under the moon, food always shows up when needed, healing happens because and who needs information when you can just bash the opponent no matter what his weak point is. In OP each friend represents an entire support caste on his own with cooking, information gathering, healing, repairing and son. With KnY, BnHA, CSM, AA, WT, UU the organization is what gives the main protagonists the funds needed to gain track on their goal. Without a smith it is pretty damn hard to repair your broken sword, without an inventor you wouldn't get the equipment needed for your problem, without governmental allowance you are just an enemy of society, without an agency it is pretty impossible of becoming a star on your own, without an organization recruiting of new agents to protect earth becomes a problem and without many little people without big powers behind them the cogs of any machinery would stop working as they are the grease to keep it going, cleaning the building, healing the wounded, feeding the heroes, preparing and repairing their weaponry, inventing and testing new stuff and so on.
In Dragonball it works without such an organization because the battles are important not the mundane stuff around it. In OP it works because every character is a genius on his field, alone able to do for what normally you'd need dozen of people. For all the other series the MC is a specialist and to be a specialist you need other specialists who support you in the fields you either suck, are average or only good in but don't actually excel at, so that you are able to focus on what you do best: Usually fighting.
At least I think that's why we got so many organizations in WSJ series but that doesn't mean that the MCs don't decide their own fate while they are in it. Since the others are too far ahead I can't use their examples as spoiler but in UU for example Andy
ignores the quest order the Union wants to go at and picks the hardest quest possible with the least reward and enlists the 2nd best fighter of Union to go with him against his will. You get similar stuff in KnY, BnHA, CSM, AA, WT and so on.
I forgot to wrote about TPN and Dr.Stone.
As for TPN I don't really agree with you that organization and organizer of fate or in my opinion decider of fateful decisions is actually in the same boat. For TPN the organization part got mostly skipped, like its there but it doesn't matter as much as what our MCs do after all. The sidecharacters who do the organization work after all don't get that much screentime and when they do they usually do outside of work whereas in KnY you'd see a healer usually doing their job, healing the MC and friends and thus interacting with them.
Dr. Stone however is a great example of how a MC builds up an organization. Starting with a sole MC, getting a partner, getting a 2nd partner, getting a 3rd, getting into a problematic head-off with a certain partner, recruiting new members to work for MC's goal while the new members just want other stuff like tasty food for example, beating the competition, merging with them, building plans upon plans upon greater and greater plans for which you need a leader with ambition and a clear goal and a mind for you guess it right organization. But even that MC ofc can't do anything perfectly which is why he gathers those partners and workers and specialists to help his plans bear fruits.
I think Dr. Stone is one of the best series where you watch the MC build an organization on his own starting from nothing but it does show how hard it is to enthuse readers reading it given its sales before the anime. It simply ain't that exciting to watch somebody build something from scratch for months or years than witness the epic result when it is finished.
At least I think this is why there are so few series like Dr. Stone with the premise of the MC having to build an organization of his own to support his goal when it is much easier to just give him a couple friends who miraculously can handle the whole rest without needing like 5-6 kitchen helpers or 2-3 smiths or what nor.
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