Even though it's a DS game, Pokemon Platnium would be a good option. It's one of the longest of the series' games, and its challenging compared to the other games. Not to mention, there are a lot of optional rules that can be added to make the game replayable hundred of times, like I have.
If it has to be a 3DS game, I'd say play Mario Maker. You can be creative, or rip your hair out over other people's impossible levels (like I do). Personally, I come back every day to play either Animal Crossing: New Leaf or Nintendogs + Cats. I like virtual pet games, and Animal Crossing is just kinda fun for me.
A few good 3DS games are Tomodachi Life and Miitopia. Both are amazing and fun 3DS games (though Miitopia can only really be played once before it gets kinda boring). Both were so well made, and I think it's anazing that some of the best Nintendo games were based off characters that were basically only used for avatars on the Wii.
In the end, it's just personal preferences. I've always loved the Pokemon series, and own all of the 3DS titles, because there's so much to do!