Undertale is this but it’s not focused on too heavily unless you play multiple routes.

Deltarune I think (I haven’t played it myself) has this kind of plot with the protagonist having an antagonist relationship to the player controlling them, but it’s more focused on player-made choices instead of save mechanics.

I would also like to nominate In Stars and Time, which is about timeloops and is very meta but not in the fourth wall breaking way.