Cool game, here are my thoughts:
I'm a sucker for variety puzzles like this one, so I had a good experience. I was definitely a fan more of the puzzles with independent concepts, but it was always fun to find a pattern and slowly see a valid word emerge. I will note, certain puzzles definitely needed some outside knowledge, such as Picross and the Platonic one, both are easily searchable and it is reasonable to assume the intended audience will have that knowledge, but it's still somewhat unfair to someone without the proper experience. The letter-to-number cipher was also a bit tedious at times, as was the Caesar, I would have appreciated being able to type directly into those decoding tools to have my message translated. Certain puzzles also felt a bit unfair in general, my major gripe was the endgame puzzle about finding a morse code word without the spaces, even trying to deduce what the first and last two letters could theoretically be left me with a ton of options, and brute forcing is arguable necessary for the solution. The abstract shape/color grid code was annoying for a similar reason due to a misunderstanding, I thought that every square corresponded to two letters, it was only after I watched a bit of a walkthrough that I saw what I was doing wrong. Just one more letter already given there would have done so much for me.
I think a few options for making the game easier without reducing the direct difficulty of the puzzles would be some subtle UI additions. Each puzzle could have a marker for whether or not it is currently solvable with the information you have available, whether it utilizes information from other puzzles, and whether it is interactable. Any of these would have significantly reduced my frustration.
The story is more of an excuse for a bunch of cryptic puzzles, but I do like how you have more revealed to you through the internal documents, hinting at the conclusion. While the RYGB throughline is good for a consistent atmosphere, I do feel it may have hurt my comprehension of some puzzles (namely pentomininos). The puzzles overall are also almost completely colorblind friendly, some small alterations could make this absolute.
Despite my many complaints, I really did enjoy this game, this was definitely a gem of a find on itch, and I am eager to see more work. Keep it up!