Exactly this. I've been thinking about how TOTK is fundamentally directionless compared to BOTW for ages. Because it's not even just the question driving the core of the game that falls flat, it's the theme and feelings it's supposed to invoke that fall flat too because TOTK has no thematic core.
BOTW is ultimately about grief, remembrance, and life continuing despite what was lost. As we explore Hyrule, we get to see the devastated ruins from the Calamity and learn about how the survivors pay tribute to their fallen and work to pick up the pieces. We get to see exactly how this unspeakable loss affected each of the different cultures, how the sudden reawakening of the Beasts is bringing it all back, and help them navigate through it all as the Hero. When you play as Link in BOTW, you feel the tranquil grief everywhere as you wander the world. It's the beating heart of the game.
TOTK is about... not really anything at all. Friendship, maybe? Uniting under a common goal? The bulk of the story is Zelda's flashbacks, and those ancient events are just about Rauru wanting to be the king of a unified Hyrule and Ganondorf resisting. And since Rauru is depicted as the hero, I can only assume this is meant to be the theme? It carries through into the Modern Era in a sense, with the flags of each of the cultures being raised in Lookout Point once you complete their quests, but it lacks any and all soul. We don't get any introspection into how all the races felt about this unionization in the ancient era, and in the modern era we're already on good terms with everyone and they're on board as soon as their people aren't at death's door. It just doesn't feel like anything, unlike BOTW's Beast quests were you got to learn about the civilizations, their histories, and how the Calamity affected them in particular.
TOTK has so, so much, but there's no thread connecting it all and it just leaves it feeling busy. The lack of a core identity is at the heart of all it's issues, because if you assign it something it gets way easier to sort it's narrative into something that makes sense.
For example, to pair it with BOTW's theme of life continuing after loss, let's make it about the perseverance of life through tragedy by focusing on the tragedies hitting all the civilizations in TOTK. With this core, we can go back to the Ancient Era and have what drove Rauru to unify the races be terrible tragedies wearing down each culture like they are in the Modern Era. Rauru decides that the only way everyone can survive is through pooling their resources and using their separate strengths to cover for the other's weaknesses, but Ganondorf opposes and thinks the only way the Gerudo will survive is if they keep their resources to themselves. Boom, now we have compelling motives for the two groups that keep the main conflict intact. Carrying this through into the Modern Era, the sage flashbacks can be about their people's separate blights and how joining together solved the problem, which ties it in to the modern Sages pledging allegiance to Link. Now it feels a lot less like the Sages doing so because the narrative demands it, and more so like they're listening to the wisdom of their ancient counterparts.
This also fixes the Zelda Problem. Let's scrap the mystery of it--what you identified as the core question of TOTK--and focus on the tragedy. How is Zelda's disappearance affecting the Hyruleans? How's it affecting the rebuilding efforts, diplomacy between the civilizations in this era of unease, the day-to-day of those in Hateno after she so thoroughly integrated herself into their lives? How can she be haunting the narrative instead of being some mcguffin to search for?
Also, slightly unrelated, but I think having Zelda's memories be locked behind Puppet Zelda fights instead of having them be just thrown on the ground around the world would make them way more cohesive story wise. Instead of the current loop of Link hearing about a Zelda appearance, not telling the quest giver that he knows what happened to her, and then going to fight the phantom just to report back like "yeah lmao not zelda" it could go like Link hearing about an appearance, letting the quest giver know right away that that isn't Zelda and then seeking it out to get another piece of the puzzle as to what exactly she went through in the Ancient Era. Just makes the effort more worthwhile.
Anyway I definitely went on a tangent there. I hope my 2 cents were interesting--i do have a lot more thoughts on TOTK still lmao. well bye!
