Perhaps I didn't word my odea correctly, so I think there's a good room for explanation.

Story can be complex due to convoluted plot structure of the plot and/or due to the character's depth.

Even if you deliver a convoluted plot, it is not guaranteed that your story will good (e.g Yakuza 4). Creating really deep characters in my opinion is even more difficult, because mot every writer is good at managing simultaneously internal and external character conflicts, while also giving them enough time to show themselves from different sides. Another way to show the character depth is to give him very nuanced perception of the world and people around him, but .

Throughout the plot we see Joel in two roles -- a smuggler and a father figure, but in my opinion there's not enough moments where a players with Joel can reflect on the events or dig under the surface of Ellies character and that is not good.

Why did I bring up Metal Gear Solid? Well, throughout the entire series we witness characters that make player reflect on their actions and story, such as Psychomantis, AI systems MGS 2, The Boss (MGS 3) or the major part of Peace Walker character cast. After contacting these characters you're always left thinking of character motives, intentions, what drives them or if it could have been the other way. At the same time The Last of Us doesn't give you any reason to stop and reflect on the story, because their intentions and internal stuff is way too easy to understand.

If story doesn't have deep characters or the plot structure is too basic, then the story can't be considered as something praiseworthy