I think most has been said already, but I'll just add my own thoughts anyway. There's some spoilers, though I try to keep things vague enough.
This certainly isn't a perfect game, but it's a game that's so amazing in what it does, that it far outweighs the problems (and it really has some).
It's more or less the game I always wanted to be playing when I was playing Tomb Raider or Uncharted. The game takes its time unfolding the narrative, and even after finishing the game for the first time, I had nowhere near a full grasp of what everything was, or what everything meant. Stories, after all, as Aliya puts it, don't have neat beginnings (or endings). But beyond painstakingly retracing my footsteps to see what I had missed in my first playthrough, my second playthrough played out wildly different. Having a better grasp of the language than the first time, and there being more elaborate sentences to translate was already enough to keep my attention, but the fact that I skipped over certain clues and found others greatly impacted the way the story played out. Both in the order in which I uncovered sites, as in the understanding Aliya got from the clues.
I also met different people (and didn't meet others). And my behaviour towards others was different from the first time too. I had started my playthrough the first time around, trying to be as kind as I could, but after most people treated me either coldly or plain hostile, I started to bark back. The second time around, I started with that banter attitude, but at some point changed my ways to be kinder again, as I was hurting others now. The difference in how conversations play out, and how organically it does so is pretty amazing. I am now on my third playthrough, and again I'm playing in a different way. Being kind helps, but telling the truth, as I've learned, certainly doesn't get you the best results. So whenever I can, I try to avoid the gaze of Iox, while maintaining my facade of kindness towards them.
The biggest problems it does have are with the traveling, both the part of sailing as the part of uncovering a site can play painfully slow. The sailing isn't really engaging and often feels like driving through a city with only one way streets. Six has messed up directions a couple times during my play time, so when I'm not paying constant attention to the map myself, I might be in for another big sailaround to get back to the current I want to see. He has a nack for calling out ruins the exact moment you passed the intersection too, so I gave up hunting them down at a certain point. While on the ground, he often asks me if I'm done with investigating, when there are still obvious parts that need to be searched, and while I'm fine with this, and I can see it as a character quirk that is deliberately written so, it's also inconsistent and at certain parts he won't ask it, when I've clearly turned the entire place inside out and there's nothing more to find. There is no way of asking him myself, so I will need to walk to the vicinity of the landing spot to trigger it.
And the game does have a tendency to waste your time like this. When discussing artefacts with Huang, he will always ask to archive the object, and walk off, letting me wait for him to get back, and honestly, I have yet to figure out what good this brings me. If I hang on to the artefacts I can trade them, or show them to others. If I let him bring them to the curators, I just lose them without gaining anything. Then he only ever has 'time' for me to discuss two or three artefacts. I can understand that this places emphasis on picking the right items with the most importance to uncovering new clues, but when I can hop over to Elboreth and back to get another opportunity, it just feels a bit arbitrary.
But all that never bothered me enough to make me stop enjoying the game. I just wanted to uncover more writing, and more lore, figure out just how this history had played out. Slowly understanding the components of the language and at a certain point understand the words better than the system of the game would let me. That was the real victory for me. It's a real gem of a game with a unique presentation, fun main gameplay hook, great way of telling a story, and a pace that few games dare to adopt, but that pays off real well.