This is something to keep in mind when praising games that manage to teach in-game concepts without floating text or explicit instruction. Games with familiar mechanics benefit from cultural context. To use an example from the OP: running. Those of us who grew up with Super Mario Bros. will be immediately familiar with the mechanic of a "run button" that exists as a modifier key to the movement buttons, but without context this is a remarkably undiscoverable concept.
This notion also penalizes games that don't introduce fundamental new mechanics over time, and instead give the player all their tools from the start of the game. Super Metroid gets away with using animal NPCs to occasionally demonstrate non-intuitive mechanics because they space these encounters out instead of front-loading them all into the player's face the moment they get off the ship.
Contrast Dark Souls, which I've seen criticized because of its use of fourth-wall-breaking how-to-play-the-game text in its opening level. But, firstly, Dark Souls is not a game that particularly cares about holding your hand (to put it mildly), and secondly its basic mechanics are more complex than Super Metroid's (though its specific choice of controls is admittedly god-awful). This is a recognition of the idea that it is more fun to actually play the game and exercise the controls than to waste your time guessing at which unknown concepts happened to be mapped to which controller buttons.
I think you're absolutely right. This touches on the de-emphasis of game mechanics in modern games in favor of story-telling (see 'The Order' as an extreme example of this -- I'm not saying this to criticize the game, I actually really enjoyed it for what it was).
I think games like Dark Souls strike a chord with people BECAUSE they have great mechanics that are fun in themselves without the need for story. For an EXTREME example of this, look at Flappy Bird. That game was pure mechanics. I'd also put Angry Birds in there as a game with very strong mechanics (with some framing elements). I think Doom is another game that did this wonderfully - to me at least, it plays very much like an arcade game.
I guess what I'm trying to get at is that I don't think it's the hand-holding per-se that presents a problem. I think what happens is that many games with very weak mechanics happen to have a lot of hand-holding, which leads us to blame the excessive hand-holding when it's just that the gamePLAY (emphasis on PLAY) was weak.
That's why I think it works fine for Dark Souls to have fourth-wall breaking text telling you how to play. The mechanics are strong enough that even when you're told what to do, actually doing it is a fun and playful challenge.
When I say 'play' what I specifically mean is - freedom to experiment within the game's mechanics to find a solution or defeat an obstacle. For that to work, the game has to provide enough mechanics and enough agency for the player to be able to explore them.
When I use the word 'mechanics', I mean anything that can be interactively explored in the game. So, a game's level design can provide mechanics. The way items or weapons work might provide mechanics, etc. A game might have really boring levels but interesting enemies. It might have no enemies and a really interesting world (Myst, for example). A game can make up for a lack of agency in one area (eg- a racing game set on real-world tracks) by providing lots of agency in another area (an interesting AI system that gives the player lots of ways to manipulate the AI in order to win).
The other factor with games like Dark Souls that does go back to hand-holding is that when you play them, you actually feel like you're becoming more skilled as playing the game, as opposed to just being really good at following instructions, or increasing some stat which basically amounts to the game artificially making things easier for you (I'm not saying this as a criticism, just as a point of difference to consider).
This notion also penalizes games that don't introduce fundamental new mechanics over time, and instead give the player all their tools from the start of the game. Super Metroid gets away with using animal NPCs to occasionally demonstrate non-intuitive mechanics because they space these encounters out instead of front-loading them all into the player's face the moment they get off the ship.
Contrast Dark Souls, which I've seen criticized because of its use of fourth-wall-breaking how-to-play-the-game text in its opening level. But, firstly, Dark Souls is not a game that particularly cares about holding your hand (to put it mildly), and secondly its basic mechanics are more complex than Super Metroid's (though its specific choice of controls is admittedly god-awful). This is a recognition of the idea that it is more fun to actually play the game and exercise the controls than to waste your time guessing at which unknown concepts happened to be mapped to which controller buttons.