Going to also have to recommend Xenoblade Chronicles. The music in that game is freaking amazing, and the story itself has so many twists and surprises to it. I was in your situation actually, I got a new Nintendo 3DS and was looking for games to play on it when I discovered that Xenoblade was a top choice on so many YouTube channels and articles. I didn't think I would like it at first, but it ended up becoming my most favorite game after I finished it.
If you do buy and play it, I highly recommend that you play it purely for the story at first and only completing quests that you come across. There are so many side quests in that game, you are most certainly going to have to use a guide to find them all... in which case you are extremely likely to accidentally spoil yourself. So yeah, do the story first and then do all the other stuff on your second playthrough pretty much.