I'm gonna go with Nier.
While it's usually highly praised by the few that have played it, even among them, there are a large number of folks who overlooked the more interesting narrative bits the game had to offer because they involved the rather fetchy quest system. I haven't seen a game that has so skillfully built a world as subtley bleak as Nier. The final ending will probably stick with me forever.
IMO Nier is one of the top 10 games of last gen. The atmosphere and world building in that game is almost unmatched. I am crossing my fingers and hoping Drakengard 3 is able to inheret some of those qualities from Nier.
Oh, and the voice acting was ace.
