I haven't played Dark Souls, but based on your explanation, I'm not sure if that's the case or you don't get hooked by the mechanical transference...As explanation compared to a different game, the next link:
It is a very similar mania that drives Dark Souls, I believe.
Yeah, most of the tropes I'm not fond of are mainly concerning the protagonist and its actions (except one I stated earlier).
That goddamn 'chosen one' trope in particular (that is the crux in so many YA-movies)...it can go ease on a cactus for a while, imo. (Kung Fu Panda subverts it greatly, though.)
Looting innocent people's homes as the hero does feel awkward, too. (e.g. Zelda, Bioshock Infinite...) I've heard Chrono-trigger did something very creative with those tropes (involving a court), although I don't have the game nor played it.
You could alleviate such things by actually have such arse-holery being punished, for example in RPGs (I think, classifying games is hard) to have (some) shop prices raised or them to close completely, less NPC's giving you gifts or helpful/vital advice, changing mood of party members or fully defecting from you...
I think it's mainly a matter of some (I'm not going to put a number here) developers not considering (so much) looking at what the mechanics they implement convey...with all its consequences, mainly immersion break.
That timer thing earlier discussed could be used greatly to increase immersion when not hidden from the player (Majora's Mask the great example of this). It could be very interesting as a challenge run, too, forcing you to complete the game before the "in-game"-timer is over (example: events take place over a week in the story, so you only have what in-game represents such a period of time to beat it)
(Could it be...? 1000th post? Yes!)