Possibly the new Zelda since we know they're working on one. The new "2D Mario" game that was teased (not the Wii U one, there was a new 3DS Mario game being teased). Perhaps a new teaser for Smash Bros on Wii U and 3DS if Sakurai has already started tests for it (seeing as Kid Icarus development ended a while back now i could see him whipping some concepts up to show off to build hype). And i'm betting Epic Mickey Power of Illusion will make its video debut there. Not to mention Project X Zone.
As for totally random ideas that i'm pulling out of my ass, some of which probably won't ever happen-
- New Sonic game
- Localization plans for Monster Hunter Tri G and maybe 4
- Yoshi's Island 3
- New Kirby game
- Donkey Kong Land Returns (lol)
- Metroid Dread (even more lol, but i'd take just about anything else Metroid as long as it's not another Other M)
- Mario RPG remake or real sequel (Square is rumored to be licensing characters to Nintendo, but it's most likely for Smash Bros, still i can dream)
- New Megaman game or Legends 3 revival (okay okay, i'm done with the impossible games jokes)
- Golden Sun 4
- The World Ends With You sequel (though i guess this could go to Wii U as well)
- Another Resident Evil
- Some sort of Street Fighter
Other than the new stuff, i'm sure we'll see new assets for Luigi's Mansion 2 as well as Paper Mario 3D. Kingdom Hearts 3D is arriving internationally in July so that's a very safe bet an English trailer will be there (most voice recording is done already). And obviously Animal Crossing. Anything known already but not out yet.
3DS games i think we will see at E3
Call of Duty: black ops 2
Dragonball Z: Budakai 3D
Epic mickey 2
The monster Hunter Games
Sonic Generations 2
A new Zelda
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next 3DS update.