The story in Nier is truly something different. It is not in any way a standard JRPG storyline. I'm not going to go into any more detail for the sake of not spoiling it, but suffice it to say, it is still something that I think about a couple of years after playing it. The character development is done really well. What really makes that matter even more, though, is that the characters themselves are so unusual and interesting. I need to really stress that it is a mature story. Yes, there is a female companion that does nothing but cuss and talk trash, but that is as juvenile as it gets--and that's just her defense mechanism, anyway lol. These are real characters with real problems that react in real ways. It adds a lot of impact to what is going on.
The music is dominated by haunting vocal melodies--vocals are usually the main focus, but it's not a capella. I have never heard another soundtrack like it, and I still listen to it frequently. It is wonderful. The world itself is interesting to explore, and there are many interesting locations to go to. The gameplay is kept interesting by some very creative boss battles and some interesting puzzle sections. It is easily one of the most criminally overlooked JRPGs of all time. It's too bad SE sent it out to die with little marketing and a terrible name.