arguably one of the best told stories in video games

It is certainly arguable, considering how I can and have done so. TLOU was good, and that's it. Nothing spectacular. Even out of 2013 I had much more fun in Saints Row IV and found a much more interesting narrative in Bioshock: Infinite.

When you're telling an Indiana Jones style of narrative, locale is key.

Not over strong characterization. Any writer worth their salt will tell you that the moment you put your characters in the back seat to brilliant set pieces, you have lost control of your story, because now the focus isn't on the people we have been getting to know thus far and whether they behave in a likable, interesting or character-appropriate way (and, by proxy, how that drives the plot), it's on the shiny stuff they're standing in front of. Characters are what link the viewer or reader to the story: I can't connect or relate to the giant mansions in The City of the early Thief games, but I can relate and connect to Garrett and his likable and interesting personality. Ergo, if you prioritize interesting locations over good characters, you're a bad writer.

I'll take the monotony of Washington DC and the engaging people in House of Cards over the flashy, cool world of the Matrix and the rice pudding characters of Neo and Trinity any day of the week.

What's intriguing for fans of this adventure/tomb-raiding sub-genre is the locations and situations the characters are put into and how they interact/deal with it.

Read that sentence back to yourself: "The locations and situations the characters are put into." The focus is on them; their struggles, their goals, their identities. As games like Half-Life 2, Wolfenstein: The New Order and Mass Effect have demonstrated, even the most standard and generic of settings (alien invasion, alternate history Nazi-world, and Star Trek-universe) can be made interesting and engaging if you put good characters on top of them.

like The Last of Us, they went for a deeper, personal narrative that focused on the human condition because that is what post-apocalyptic narratives should be focusing on.

I agree. Although that doesn't stop me from saying that a zombie apocalypse setting is such a dead horse that even its grand-colts were miscarried.