A new sidescrolling Metroid, perhaps covering the post-Fusion storyline since the events of that game could fundamentally change Samus' role in her universe. Metroid Dread or whatever you want to call it, i want a new sidescrolling Metroid game that occurs after the GBA one.
Smash Bros. Assuming they can recapture the brilliance that was Melee, i'll take this one without any hesitation.
Kirby. I'll take a new one or an old one, preferably a new one. BTW, Kirby has never made the leap to the third dimension (in terms of exploration, like Mario 64) except in his racing game. Perhaps it's about time to give it a try. I'd never say no to a sidescroller though! I'd even take a remake of Dreamland 2 or 3 since they've not been milked as much as the rest of the series. Dreamland 2 was really brilliant, it was my first GB game, AND my first Kirby game.
Since there's hope of reviving the DKC franchise, lets hope another game makes it onto 3DS if the Wii version is a success. They even put some DK props in the 3DS E3 promo.
New 3D Mario game (3D in the sense of exploration, not the effect). Although i'd take a remake, you can keep your Galaxy or Sunshine. How about a brand new 3D platforming Mario title?
And if the retro remakes go well, i'm hoping we see some love for Super Metroid, DKC trilogy, and Mario RPG. I feel all 3 of those games would look really awesome with a 3D-makeover (3D being the effect).
Final Fantasy 5 and 6. Now that we have graphics at least on par with the best of last gen, the time is perfect for these. They cited tech issues as holding DS versions back, but i think they just knew the 3DS was coming and they intended to keep their eye on it. Can you imagine these games with Gamecube-caliber visuals or better? I can, and it's epic.