You know it's always hard to pin point what games most of the studios at Nintendo are working on. I thought we can all make are guesses in this topic though and feel free to add in possible third party studios if you want. Here are my predications even though I'm likely wrong.
Kyoto office
KSD group 1: I believe there working on a Nintendogs for mobile and are in the planning stage for Mario Kart 9 for NX.
KSD group 2: Splatoon updates and Animal Crossing amiibo Festival. I believe there also in the planning stages for Animal Crossing NX and a Mii title for NX.
KSD group 3: The Legend of Zelda Wii U and Tri force Heroes. They might also be in the very early stages for an NX Zelda game.
KSD group 4: It's possible there working on Super Mario Maker DLC. I also think there in the planning stages for New Super Mario Bros NX and Pikmin 4.
KSD group 5: Star Fox Zero with Platinum Games. They might also be working on a Wii Fit title for mobile or NX.
Tokyo Studio
TSD group 1: Overseeing the next Zelda remake.
TSD group 2: Working on a new 3D Mario for NX with 1-UP Studio.
Second Party Studios
Monolith Soft: Working on a new Xenoblade for NX most likely.
Nd Cube: There leading a hand with amiibo festival and could be working on a Mario Party for mobile. They could also be in the planing stage for Wii Party NX.
Retro Studios: I think there in the planning stages for Metroid NX and Donkey Kong Country NX.
AlphaDream: Mario & Luigi Paper Jam.
Ambrella: Pokemon Rumble for NX or mobile.
Camelot: Mario Tennis Ultra Smash and there likely at work on Mario Golf Wii U as while.
Game Freak: Pokemon Z with Creatures Inc.
Genius Sonority: Pokemon Shuffle for mobile.
Good Feel: New Yarn game for NX.
Grezzo: Next handheld Zelda remake
HAL Laboratory: Kirby Wii U or Kirby NX
Intelligent Systems: Fire Emblem Fates DLC and overseeing GIR X FE. Also in the planning stage for Paper Mario NX.
Monster Games: DKCTF port for New 3DS or Diddy Kong racing 2.
Next Level Games: Metroid Prime Federation Force. I also think there working on a small Wii U project.
Skip Ltd: Chibi-Robo Zip Lash
Third Party partners
Sonic Team: Next main Sonic game for Wii U and 3DS
Sega Sports Japan: Mario & Sonic at the Rio 2016 Olympic Games.
Samzaru Games: Sonic Boom Fire & Ice.
Capcom: Monster Hunter series and a new Mega Man game for NX.
Bandai Namco Entertinnment: Super Smash Bros Wii U & Nintendo 3DS DLC with Sora Ltd. and Project Tressure. I also think Namco will make Smash 5 for NX.
Platinum Games: Star Fox Zero with KSD group 5. I think they will also make Wonderful 102 for Nx.
Square Enix: Mario Sports Mix Wii U.
Kyoto office
KSD group 1: I believe there working on a Nintendogs for mobile and are in the planning stage for Mario Kart 9 for NX.
KSD group 2: Splatoon updates and Animal Crossing amiibo Festival. I believe there also in the planning stages for Animal Crossing NX and a Mii title for NX.
KSD group 3: The Legend of Zelda Wii U and Tri force Heroes. They might also be in the very early stages for an NX Zelda game.
KSD group 4: It's possible there working on Super Mario Maker DLC. I also think there in the planning stages for New Super Mario Bros NX and Pikmin 4.
KSD group 5: Star Fox Zero with Platinum Games. They might also be working on a Wii Fit title for mobile or NX.
Tokyo Studio
TSD group 1: Overseeing the next Zelda remake.
TSD group 2: Working on a new 3D Mario for NX with 1-UP Studio.
Second Party Studios
Monolith Soft: Working on a new Xenoblade for NX most likely.
Nd Cube: There leading a hand with amiibo festival and could be working on a Mario Party for mobile. They could also be in the planing stage for Wii Party NX.
Retro Studios: I think there in the planning stages for Metroid NX and Donkey Kong Country NX.
AlphaDream: Mario & Luigi Paper Jam.
Ambrella: Pokemon Rumble for NX or mobile.
Camelot: Mario Tennis Ultra Smash and there likely at work on Mario Golf Wii U as while.
Game Freak: Pokemon Z with Creatures Inc.
Genius Sonority: Pokemon Shuffle for mobile.
Good Feel: New Yarn game for NX.
Grezzo: Next handheld Zelda remake
HAL Laboratory: Kirby Wii U or Kirby NX
Intelligent Systems: Fire Emblem Fates DLC and overseeing GIR X FE. Also in the planning stage for Paper Mario NX.
Monster Games: DKCTF port for New 3DS or Diddy Kong racing 2.
Next Level Games: Metroid Prime Federation Force. I also think there working on a small Wii U project.
Skip Ltd: Chibi-Robo Zip Lash
Third Party partners
Sonic Team: Next main Sonic game for Wii U and 3DS
Sega Sports Japan: Mario & Sonic at the Rio 2016 Olympic Games.
Samzaru Games: Sonic Boom Fire & Ice.
Capcom: Monster Hunter series and a new Mega Man game for NX.
Bandai Namco Entertinnment: Super Smash Bros Wii U & Nintendo 3DS DLC with Sora Ltd. and Project Tressure. I also think Namco will make Smash 5 for NX.
Platinum Games: Star Fox Zero with KSD group 5. I think they will also make Wonderful 102 for Nx.
Square Enix: Mario Sports Mix Wii U.