If the quandaries you describe were more front and centre, and if they tied better into the main progression of the story, sure, you'd have yourself an argument. The problem is, these examples are all relatively isolated from the core of the story, and most of them are shallow.
Example of the "Literary" way that "Issues" are handled:
To Kill a Mockingbird.
What about character interactions in ME? They're shallow, too. This can be excused if, for instance, you're focusing more on the experience that the characters are going through, rather than on the characters themselves.
Example of the "Literary" way that "Character Experience" is handled:
The Shadow of the Colossus.
Spoiler It's a very simple story. A man goes on a journey to bring his love back from death. The whole game is about this and this alone. It's "Literary" in the "Classical" sense; there are countless stories of a similar vein.
Want a more contemporary example?
The Human Stain.
What about complex character interactions, you say?
Examples of the "Literary" way that "Character Interactions" are handled:
Closer or
Who Killed Virginia Woolf or
House of Sand and Fog.Some stories are "Literary" mostly because they are so original and originally conveyed. ME certainly isn't original.
Example of "Literary" originality: China Mieville, Haruki Murakami.
Spoiler (Although, Haruki Murakami's stories are also extremely personal and inter-personal narratives, concentrating on a few and people relationships with constrained precision. And China Mieville's stories are just weird, full stop.)