Just for the hell of it, here's the list of remaining IPs that are not used for 3DS/Wii U

Wii U:

1. Pokémon
2. Pokémon Rumble(Ambrella, Rumble series' developer has a Pokémon patent for now, presumably for Wii U. For Gen VI).
3. Animal Crossing  Animal Crossing: amiibo Festival was revealed on June 16, 2015.
4. Metroid
5. F-Zero(Lol)
6. Chibi-Robo!(has a 3DS eShop game, but no console game since GC save for Wii rerelease)
7. Kirby
8. Wario Land
9. Fire Emblem(not counting SMTxFE).
10. Mario Tennis(GC game was rereleased for Wii) Mario Tennis Ultra Smash was revealed on June 16, 2015.
11. Mario Strikers
12. Mario Baseball
13. Paper Mario(Paper Mario: Color Splash was announced March 3rd).

Nintendo 3DS:

1. Pokémon Mystery Dungeon(For Gen VI)  Pokémon Super Myster Dungeon was announced on May 21st, 2015, to be released in August 2015.
2. Metroid Metroid Prime Fedaration Force was revealed on June 16, 2015.
3. F-Zero(Lol)
4. WarioWare WarioWare Gold confirmed for August 3rd, 2018.
5. Wario Land
6. Pokémon Rumble(see above) Pokémon Rumble World for 3DS was announced on April 1st, 2015 to be released on April 8th, 2015.

Others:

1. Console release of Pokkén Fighters. Wii U release was announced for Spring 2016 in August 21st, 2015.
2. Mario and Sonic at 2016 Rio Olympics.  Announced May 31st, with unknown release date.
3. Advance Wars
4. Golden Sun
5. Game &Watch(Lol)

Edit(01/04/2014): Removed Pokémon Rumble from 3DS list.

Edit(21/05/2015): Removed Pokémon Mystery Dungeon from 3DS list.

Edit(08/06/2015): Removed Mario and Sonic at Rio Olympics as it has been anounced.

Edit(16/06/2015): Removed Metroid for 3DS and Mario Tennis for Wii U. Removed Animal Crossing for Wii U.

Edit(24/10/2015): Removed Console Release of Pokkén Fighters because it was announced a few months ago.

Edit(04/03/2016): Removed Paper Mario from Wii U.
Edit(08.03.2018):