So I just read this quest (though only small samples of comments). Quite intriguing. The world and characters have a lot of work put into them, and there's a real sense of danger and fog of war. Definitely deserves more attention.
There's been something I've wanted to mention for a while as I read through the quest, and hopefully I can present it without stepping on toes as a newcomer. I also see that it has boiled over recently (perhaps making this a bad time to bring it up). To wit: I fear that the control the players have is not reliable or suited to the actual environment. The QM's have a tendency to take directions like 'go east' and sometimes have Hazo cleverly diplomance his way past border patrols while stocking up on important supplies, sometimes robotically walk off a cliff, and sometimes get pissed off and go north to kick Hanzo the Salamander in the gonads. I appreciate that part of the 'rational quest' idea is that if players do something wrong there are consequences, and furthermore that writing and GMing are both very complicated things to do, so I don't want to give the impression that I don't appreciate the effort or difficulty. Nevertheless I think that having the QM's give a bit more charity to the intention of a plan might be preferable. Currently there's a strong sense of 'gotcha' when the players forgot to clarify the 27th line in their otherwise exhaustive plan. Sometimes this is legitimately a mistake, and sometimes it's just a mismatch between the rules (like keiko and social skills), the world models, or just sheer memory and effort. When the QM's don't want to make there be major consequences they just have a character (or all of them) mock Hazo for the idea (it was funny the first few times, but kinda grating from then on). All this leads to an adversarial relationship where the players are paranoid about leaving anything out and need to fill their plans with legalese and define common sense. The plans in this quest are already significantly more complex than any other quest I've seen. So making a giant common sense flowchart that is included in every plan and must be explicitly overridden to be bypassed is the best idea I have to control the crazy mars rover that is Hazo, but I hesitate to advocate for this sort of control. It's bound to have undefined edge cases, contradictions, etc. This is becoming a cautionary tale about the difficulty of defining proper behavior in every situation -- aka why gofai was never going to work. On top of that there was most of a chapter banning giant list production which may or may not be entirely humorous
Meta knowledge is also a difficult grey area, like are players allowed to mention Kabuto's use of challenge response code way back when? Or would Hazo never have noticed it because he doesn't a priori expect Kabuto to be a spy like we do? Have the players been too trusting of Jiraya because of canon expectations?
Yagura's ability to kill Hiruzen is very concerning and indicates a significant increase in Bijuu power to me.
Uchiha representative mentioned reminds me that we don't know anything about how the Uchiha clan differs in this story from canon.
Pangolins are allies, but I'm concerned about their extremism re enemies.
I still have no idea how much to believe of Kagome's exposition dump.
Lupchanz kinda sounds like Zetsu. Also the description of what happens when Lupchanz infect an infant kinda sounds like what players do to Hazo. Also possibly root agents / scorch squads ('whatever they do to make their eyes look like that').
I'm confused about the laws / rules regarding summon realm, and sealing in the summon realm. How banned (if at all) is it? Why were the summons going to copy our seals stored there if its banned? Is sealing in summon realm safe? Can Keiko bring the rest of us with her to summon realm? Where do you reappear when you return from summon realm? What if there's an obstacle? Can you just send the summon / items back? Jiraya uses this for travel, why not teleport bombs?
However, regardless of the circumstances, you are our team leader, and you deserve a certain amount of respect from us."
Which was a load of crap. Nobody deserved respect for being a team leader.
No, you can't use clear communication jutsu for social lying Hazo, that's corrupting its entire purpose.
The fact that more words are spend on criticism than praise is not an indication of appropriate allocation, praise is just harder to meaningfully formulate.
There's lots more to say (about a pretty long quest), but much of it is no longer relevant, and some will have to wait.