OP, I don't buy your insistence that TLOU's story and gameplay are incongruous with one another. In fact, I think they reinforce each other quite well. You don't really provide any good argument of why you think the combat sections are out of place, especially when the game does a great job of contextualizing practically every combat encounter. Joel and Ellie aren't even hyper aggressive, if they could've gotten to the Fireflies without any fighting they would've preferred it that way, but they were preyed on by larger groups...which is exactly how an apocalyptic scenario would play out. Besides, thereviews are plenty of segments of the game with very little combat.
With that said, making the game an RPG doesn't solve any of the issues you are suggesting the game has.