Well, now, decades later it s clear Myst is intellectually an Everest to most people, and all they did was stare up in uncomprehending awe.
Twine and other interactive fiction engines provide this to some degree, though I think Cyan’s visual aesthetic is also intrinsic to the feel of the games.
Games like 'What Remains of Edith Finch' handles the literary and primary source based diegetic narrative, with games like Firewatch or similar expanding on the premise as genre-games. Then you have the likes of Journey or To The Moon serving to upturn expectations on concepts of traditional narrative and structure, and things like The Stanley Parable satirically prodding the nature of choice and narrative viz a viz a player's actual agency.
In the ghetto of SCUMMWare point and click games with cartoonish graphics and themes I'm sure Myst was a breath of fresh air. Intellectually, however, any number of games make it look like a remedial student.
Take 'The Fool's Errand'- a 1987 computer game by Cliff Johnson which presents itself as a point and click meta-puzzle with an overarching narrative extrapolated through various visual and logic puzzles and a cryptic treasure map. The game is structured as a storybook divided into five parts, each containing a large number of different chapters; the storybook can be paged through and read as continuous prose on screen. Starting to sound familiar? No doubt, as both it and Myst lift a lot of their inspiration wholesale from Masquerade by Kit Williams
https://en.wikipedia.org/wiki/The_Fool%27s_Errand https://en.wikipedia.org/wiki/Masquerade_(book)
Jumping back to the soft-core philosophical gum-chewing, we can see the same themes emerge in a far more articulate sense as early as the Gibson/Dick-esque dystopian nightmare of Deus Ex in 2000.
Deus Ex played with any number of interesting literary vehicles including a 'novel within a novel', the agency of man vs AI and its textual interaction with the world, the inversion of symbols and signifiers, and a huge debt owed to both Gravity's Rainbow and Foucalt's Pendulum structurally and thematically. Hell, G.K. Chesterton's metaphysical thriller 'The Man Who Was Thursday' is included in excerpts throughout the game simply for flavour!
Nowadays there's plenty of easy and lazy comparisons to make based on similar mechanics and core gameplay loop - The Talos Principle or Soma for example - but I'd go more recently with Disco Elysium, which owes huge amounts thematically to China Mieville's 'The City and the City' and Émile Zola's 'Germinal'. I would like to go on (for thousands of words) but I would only spoil people's enjoyment of a TRUE creative literary tour de force and game that requires appropriate and actual intellectual rigour to engage with.
Closest thing I’ve found to the wonder of exploration, puzzle solving, and gradually unearthing a story.
Another one to look at would be Heaven’s Vault.