AlphaSapphire and Smash 3DS are great choices. Haven't played the others.
If you wanted to be clever, you could get a used copy of AlphaSapphire or OmegaRuby and transfer the previous owner's Pokémon to the Pokémon Bank service, then back to either the game of origin once you restart it, or Y. Pokémon Bank costs $5 for a year's "subscription".
You should download Pokémon Shuffle from the eshop. It's free and is pretty fun.
And if they still have the OmegaRuby/AlphaSapphire demo up, DEFINITELY download that. Just for completing it, you get a free Glalie with its mega stone for use in OR/AS. It also lets you try out all three starters and their megas if you play it again, and you get items to transfer over if you complete it multiple times.
As far as retail games go:
Mario Kart 7 is great. I'd say it's the second-best in the series after MK8, but I never played the DS one, so maybe I'm wrong there.
Super Mario 3D Land is fun, and doesn't suffer from the 3DS controls at all.
Fire Emblem: Awakening was a fun time (I put over a hundred hours into it), but if you haven't played any of the others, I'd highly recommend emulating Sacred Stones and Fire Emblem (no subtitle) for the GBA and Path of Radiance for the GameCube before playing Awakening.
I've heard that Mario and Luigi: Dream Team is pretty good (most say it's better than Partners in Time and about equal with Bowser's Inside Story, but not as good as Superstar Saga), but I haven't played it.
Sonic Lost World (legitimately one of the worst games I've ever played)
Paper Mario: Sticker Star (nothing like the original or Thousand-Year Door and RIDDLED with design problems)