I felt like the enemies were different enough that they were more then "reskins" as they made you change up your fighting playstyle. Plus, there were a lot of different enemies alone that I was constantly surprised at during my playthrough. I never got tired of fighting enemies over and over so I can't agree with this analysis of the gameplay the way you put it. Coming from BOTW or even Horizon this game has a slew of enemy variety not even including the reskins. Only the Trolls felt like reskins honestly.
It's nitpicky from the sounds of it to me. I guarantee you had there was half of the stuff you complained about missing you'd probably feel the game is empty. I personally enjoy the blue chest puzzles as some of the vases are cleverly hidden.
I agree that some of the blue chests puzzles were well done, but the ones that annoyed me were the ones later in the main story where they werent really hidden at all behind any puzzle, they were just in some weird part of the environment. Early game is where they had you move stuff to find them, or deal with moving parts and use precise timing with your axe. Then they ran out of dev time and didnt hide them behind any puzzles.
Plus I didnt play BOTW or Horizon so I guess it could be worse. But im not sure what the big variety is. There were a few sub classes of each enemy type but not enough to really engage me. I will say though since I put it on easy mode it probably made the repetition worse since I didnt really have to use any brainpower for the fights so it just felt like waves of the same shyt over and over. Id imagine it would be even longer on normal or harder difficulties which is why I didnt even bother after the first few hours and put it on easy. But the waves really do bother me, it was the same problem in Mass Effect Andromeda. I can name at least 6 times where you are in one room/elevator/boat etc where you just sit there and fight wave after wave after wave. Doing this once or twice for excitement and tension is cool, but after the 5th or 6th time its just artificially lengthening the game.
While I am nitpicking I felt like any time I was in combat for long periods of time were the worst parts of the game. The story and exploration and the world were the highlights. I probably didnt like it much either since Im not a big fan of these types of combat systems in 3D games. If it wanted to be an action game, then be an action game, ie Ninja Gaiden, Bayo, or the old God of War games. But with how well done the story is it felt like OK now its time to take a break from this experience and be a video game and make you fight a bunch of shyt for a long time.
To be really honest I would love to see a JRPG with turn based combat with this kind of budget and attention to detail to the world. Of course I dont expect this from this game but I would love to see it one day from a big JRPG dev.
And again these arent dealbreakers, Id still say this game was excellent and a must play for all gamers.