I'll second Fire Emblem and Zelda: LBW. The others mentioned are all very good, but those two in particular are personal favorites. Mm, those two and Animal Crossing. And okay Mario 3D Land was incredible. Oh and if you're going with a Pokemon game, might as well wait a sec and get him Omega Ruby. Ruby not Sapphire. Groudon, not Kyogre. It's a no-brainer. If your nephew doesn't love Groudon, then he doesn't deserve to have you as an uncle.
Might I also add that Smash Bros, while supremely fun, also inevitably broke my circle pad? I wasn't playing too vigorously when it crackled off, the thing was just wafer thin and not built to withstand so much cumulative stress. If you get him Smash, warn him of the peril. In remembrance of me.