My favourite 3DS game is Virtue's Last Reward because it truly has the number #1 greatest story of any video game ever made (the second best story is from its predecessor, 999: 9 Hours, 9 Persons, 9 Doors) and it's just so freaking incredible and I bloody despise the fact that nobody has heard of it.
My next favourites are Mario Kart 7 and Animal Crossing: New Leaf.