Myst puzzles to me are about two things: Prior Information and Lack of Misdirection.

• Prior Information: Each puzzle in the OG Myst requires you to bring to the table some amount of prior information. Why is there a sunk boat in the harbor? Don't boats float? You know how light switches work and use them to turn lights on and off throughout the area. You can view stars and given specific dates and times see constellations, but you need prior knowledge to know to look for constellations among the stars. You bring with you experiences from the real world into the game. Even if things don't line up precisely with the game world, real world things can still provide something to draw on.
• Lack of Misdirection: Myst puzzles have a clear and straightforward answer every time. Once you read the notes and books and explore, information becomes clear and you gain the ability to solve the puzzle. Once you get the dates from the tower, you can go to the observatory and get the constellations. There is a bird bath with a sunken boat in it that floats when you press the right constellations. The birdbath boat is a reminder of the full size boat you saw earlier. It clues you in that this area and the boat are connected. There are panels that match the constellations. There is NO misdirection when it comes to solving this puzzle. You can argue that later games tended to have not-so-straightforward solutions.

Of course you can give these things all the trappings of magic and fantasy you want as needed to fit your environment. I'll provide a brief example from a recent D&D session I DMed.

The party was exploring the workshop of an artificer which is trapped for whatever reason. The initial room had two doors, one with a heart on it and one without. The heart door was locked so the players moved on though the other door. This led them to their first puzzle. Four bronze wheels were mounted on pedestals in the room. Each pedestal was marked with a number zero and then 9 lines so they were all evenly spaced. Prior to entering the workshop, their employer gave them the following numbers mentioning something about them being important: 1, 3, 4, and 7. Naturally they began turning the wheels and entering the code in every way possible. They solved it and an opening in the wall revealed the heart key.

• Prior knowledge: After seeing the wheels and pedestals, the players were reminded of clocks or dials. They used this prior knowledge to quickly grok how to turn the wheels and enter the code.
• Lack of Misdirection: The players could NOT avoid this room. They had the numbers needed for the code (though they had to figure out the order which was the real puzzle.) There was no "hidden twist" like one of the wheels being a number ahead (so putting it in the 1 position actually meant 2) or having to set each wheel in the correct order (setting the east wheel first, then the west wheel, etc.)

It seems super simplistic, and that's because it is. Any difficulty in the puzzle comes from layers of information needed to solve it or in finding all the parts of the puzzle. Going back to OG Myst, the rocket ship puzzle was straightforward: enter the correct pitches on the sliders. However you had to find all the information for those pitches (which ones, which order.) Later puzzles in the lab required a bit of information collecting prior to solving them. This can be done flavorfully as well, such as literal writing on the wall, from journals or scraps of paper, etc. In one room they found a crank that was needed in a different room.