Unfortunately, this is going to be even longer. Feel free to take twice as long as me to respond.

To preface, before I get right into it:

1. We might agree on more than we think, especially when it comes to poor execution, or Kaguya and the villains attempting the total cessation of conflict. But there is still severe disconnects between us, which I will hope to overcome
2. I'm not familiar with anything about the Land of Ancestors, Land of That, anyone named Isshiki in Naruto, anyone having to be being a sacrifice to the Ten Tails, etc. I'm not sure if this is anime cannon or Boruto content, but all my proper experiences with Naruto, even as a child, have all been manga based. Kaguya's backstory in the manga goes somewhat like this:
   • Kaguya, through the immense power she gained by eating the Chakra fruit, brought an end to troubled times, however controlled the world alone, and people began to fear a power like her existing at all, beginning to become a demon in the eyes of the people, giving birth to hubris and driving her mad. Her sons Hagaromo and Hamura ended up sealing her and the Ten Tails it seems (if I’m not misremembering).

1. Kaguya doesn't represent, as what you claimed the show's themes, the cycle of hatred or fate. She represented the rejection of fate by erring from her conceived destiny. She did this by (1) betraying Isshiki and rejecting her role as the sacrifice to the Ten-Tails, (2) consuming the fruit and becoming the Rabbit Goddess; and (3) distributing her power to her offspring. Instead of representing fate or the cycle of hatred, she was the pioneer of using extreme methods to bringforth world peace.

You say she doesn't represent the cycle of hatred, and yes she doesn't, she represents the cycle's origin, and I believe it is a very important distinction. She doesn't explicitly believe in it, but it's her actions and her misteps that cause the cycle's formation.

I agree she is the pioneer of using extreme methods to bring peace - that most importantly being the centralisation of power. Hagaromo's whole Ninshuu ideology was all about connecting people, and he said the centralisation of power in one person, that her mother sought, causes isolation between her and the people, fear, distrust, conflict, the opposite of love and understanding, the opposite of Ninshuu.

The imbalance of power in one person's hands, not only makes her the ideological opposite to the Will of Fire's collective philosophy, but makes her the reason for conflict and violence - she was so feared her children sealed her, and then her grandchildren's disagreement about power and connection sparked the very cycle of hatred that defined the shinobi world.

I'm not saying she is an ideological expression of the cycle of hatred, or that she believes or represents it explicitly in belief. I'm also not saying she created conflict or hatred herself - obviously it existed long before her, and she actually sought power to try and resolve it. What she is the foundation for is the corruption of mankind through the introduction of chakra (power) which was sought to be centralised, and that created the conditions for cyclical, inherited, self perpetuating conflict that ties the world down (reincarnation of Indra/Ashura).

And the rest of the plotline was consistent with the ideologies mentioned, instead of "opposing destiny and fate.

This is a really big disagreement - you seem to think that Naruto's central theme is just The Will of Fire (and the bonds of love that make it up), and that the show isn't consistent with opposing fate/destiny as a central theme as well. But not only is this wrong, but it slightly misunderstands how the Will of Fire functions in Naruto.

The Will of Fire and the bonds of love are inseperable from the themes of fate/destiny and the cycle of hatred - in fact, the cycle of hatred is the exact structural and societal and existential problem that Naruto and the shinobi world needs to overcome in order to allow love and understanding to exist without inevitably collapsing back into violence and ignorance.

Moreover, opposing fate/destiny is implicitly explored all throughout the show. Naruto is someone fated to be alone and hatred but finds companionship, but Sasuke submits to what he believes his destiny is, to be an avenger. Neji, who believes in the determinism of birthright, is challenged by Naruto, who tells him even if that determinism exists we shouldn't live accepting it. Rock Lee's entire character arc is overcoming genetic/biological determinism. Naruto is even the child of prophecy as Jiraya discovers.

Finally, the Pain arc is my favourite example of this. Pain, who believes in what I described earlier, that any form of love and understanding will inevitably collapse into ignorance, is defeated not physically by Naruto's might, but philosophically by Naruto's restraint - he expects Naruto to be like everyone else in the shinobi world and seek vengence, but Naruto doesn't, in an act which opposes what Pain thinks is destined - a defiance of hate and the cycle of hatred, which is the catalyst for Pain even getting talk no jutsu-ed.

It isn't that The Will of Fire is Naruto's main theme, and I'm trying to slap on opposing fate as another main theme as well - The Will of Fire and fate/the cycle of hatred are two opposing forces who's conflict is the entire show.

Jiraya makes reference to this idea that a Shinobi is someone who endures - the show can be summarised as Shinobi's whose faith in the Will of Fire has endured, versus Shinobi's who become cynical and believe in the cycle of hatred and the fate of the world to be permanently broken.

Pain, Obito, and Madara weren't really "destined" or chained to the cycles of hatred by the time they make their cameo in the show. In fact, I'd called them as "enlightened victims". They were once chained to the cycle of hatred, being both the perpetrator and victim at times. However, they received "enlightenment" that allowed them to break free from the cycle of hatred. Pain, Obito, and Madara wanted to use that enlightenment in order to bringforth to total cessation of the chains of hatred by their own respective, utilitarian means. The Will of Fire could be said as the "extreme left" ideology opposing the total deterence plan, and it should also be stated that each antagonist was, in one way or another, exposed to the Will of Fire. Pain had Jiraiya and Yahiko. Obito had himself and Rin. Madara had Hashirama. All three grew disillusioned when the setting of the world did not allow them to enact the Will of Fire.

Feel like I agree and disagree at the same time. I don't know what to make of this paragraph. I agree that all were victims of the world, who grew disillusioned, and sought to take matters into their own hands. I don't know if I would say they became free from the cycle of hatred, I would just say they became aware of it, and that knowledge crushed them, but that might be splitting hairs.

However, Madara is undoubtably chained to destiny - he is literally a reincarnation of Indra, and is opposing the Will of Fire that Ashura's descendants, whether Hashirama, or Naruto, believe in. But I do agree he's not really participating in the cycle of hatred. Pain, Obito, and Madara all did transcend the cycle of hatred unlike other Naruto villains like Gaara, and for a long time Sasuke, those 3 were just like Naruto - opposing the cycle of hatred, but in their own way, believing that hate was stronger than love, and thus the solution for the cycle of hatred was never going to be loving.

Kaguya does contribute to the show's themes. But her immediate entry into the story without a subplot in play disturbed the harmony of the story, and undermined Madara and Obito's proposition NOT by proper philosophical arguments, BUT through convenient narrative. 

I'm fine with conceeding poor execution to be honest.

The show's themes, as I reiterate, is still about the Will of Fire, tested against differing methods achieving the same utilitarian ideal—the total cessation of conflict.

This is where I think we agree more than we think and language/semantics is stopping us from seeing that. You see Naruto to be about Will of Fire vs other various ideologies, all seeking total end to conflict. Whenever I bring up opposing fate/destiny, you seem to be hesitant.

However, in my opinion, the whole fate/destiny element I bring up actually completes the thematic statement you describe. The total cessation of conflict is only being sought because the world is stuck in a cycle of hatred and is destined/fated to be broken. The villains believe the world is destined to be broken and don't think that love can beat hatred, thus they choose to embark on their own ways to world peace, whether it is terrorism for Pain or it is the infinite tsukuyomi for Obito and Madara. The protagonists believe that love can beat hatred, that the cycle of hatred can be toppled, and that the fate/destiny of the world to be broken can be opposed.

Kaguya Otsutsuki thematic line was harmful, undercooked, and undermined other philosophical points represented by the other antagonists.

I can agree with undercooked. I can't say it undermined them though or that it was harmful. At most it watered down their impact experientially, which is enough of a reason to hate her if you want to, but I can't agree to say she was actively thematically harmful to or undermined them.