Two initially jump to mind for me.
Outer Wilds took me three attempts to get into, but when it did…wow. Its a game that I is definitely more than the sum of it’s parts, and one that I’d argue is genuinely beautiful in it’s story and how it tells that story.
That said, once you’ve worked out the games mystery; it’s story, it’s tricks, timing and logistics, I wonder how more pull the game would have.
Return of the Obra Dinn is a game that I spend a lot of my time thinking about. The music, the atmosphere and of course, the games moment to moment gameplay.
Those puzzles will likely (hopefully) melt from my mind at some point, but even then I fear that initial sense of excitement and intrigue will be lost.
As much as I plan on going back to it at some point, I’m not sure a game of it’s nature is all that well suited to additional playthroughs unfortunately.
The gameplay is pretty unique in this one, and the world is enormous, so a long tutorial makes sense. Once you final escape the snowy mountains and can access the wider world you feel a real sense of release and freedom that’s really worth it.
That said, like skyrim, it makes a new game a slog and I wish you could skip it on subsequent play throughs.
I don’t know if you’re on PC, but if you are I imagine there are plenty of clean save files available on the Nexus that are just post-intro.