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Well, for story I'd recommend the Professor Layton games as well as the Ace Attorney series. You can get the first three AA games on the eshop pretty cheap and the 3DS is DS backwards compatible so you can just pick up the entire Layton series used if you want to.

None of those is a jrpg though, Layton is a puzzler and AA are visual novels with point n' click elements.

People have been recommending Xenoblade Chronicles and I can second that it's an amazing game.
Also you bought the pokemon machine. How about some some Pokemon then? There will be six games to choose from shortly.

If you like Fire Emblems gameplay, but not the story, maybe try out Awakening. I hear the story is better.

Although I have to say, if you don't like cheesy drama jrpg might just not be the genre for you.