I'm about halfway through the story (something like 35% total completion) and I definitely agree with your points on the game mechanics. I'm loving the game as well, and I think the fact that HZD shines in so many areas actually makes it a little easier to notice the shallower parts of the game, or stuff that feels like it should be there but isn't. The rest of the game is so massive and deep it's hard not to notice.

Overriding definitely feels like there was probably supposed to be more to it that maybe was cut, since going through the cauldrons is such an intricate and cool way to get the upgrades.

I was a little surprised you couldn't fly either (but like, I get it since there's probably no way the game could keep the graphics looking this good if you were moving through the world that freely), but I would've just settled for being able to rappel everywhere. Running around the mountainous areas would feel so much cooler if you could just leap off a cliff anytime you wanted to, or grapple up to ledges. The weird way you can instead "skyrim-hop" up and down cliff faces just looks goofy in such a polished game, I guess.