Retro Studios is probably working on the next Donkey Kong game.

F Zero another possibility for Retro is they're the company that resurrects old IP.

Retro only had their last project released four months ago. They are, at best, six to eight months into development of a new title. To give some perspective of development practises at Nintendo, Miyamoto's Starfox, Giant Robot and Project Guard prototypes are six to ten months into development, and it's unprecedented that such early prototypes have been revealed and were playable at E3. We'll see Retro's next project next year at the earliest, I think. It's also possible they're working on two projects, either two of their own games, or their own game and assisting with development on another title that Nintendo want finished on time. Perhaps Zelda or Smash.

As someone else has pointed out, Pokken Fighters/Tournament also hasn't had an official unveiling, so that's another Wii U title floating around somewhere. Monolith Soft's 3DS project also hasn't been unveiled; presumably it's all hands on deck to finish Xenoblade Chronicles X. Also, Next Level have been free to work on another title for over 12 months now, and are basically a Nintendo exclusive developer, so that's another 3DS or Wii U title unaccounted for. It could be they'll be given the Star Fox prototype to finish, given Miyamoto worked with them on Luigi's Mansion 2, unless they're hard at work on something else.

Project Steam's development is not interfering with Fire Emblem x Shin Megami Tensei, that was one of the last topics of conversation during the roundtable.

Presumably, at the moment:
EAD Kyoto teams are working on Splatoon, Zelda, possibly Mario Maker, Project Giant Robot, Project Guard, and looking for a development partner for Star Fox (also wrapping up Hyrule Warriors oversight duties);
EAD Tokyo are working on Captain Toad and possibly the next 3D Mario;
Monolith Soft are working on Xenoblade Chronicles X and possibly a 3DS title;
Intelligent Systems are working on Project STEAM and co-developing Fire Emblem x Shin Megami Tensei;
Sora Ltd are working on Smash with Namco;
Nd Cube are presumably behind Mario Party 10;
1-UP Studio presumably assisting on projects;
HAL Laboratory are developing Kirby and the Rainbow Curse;
Game Freak are working on Sapphire/Ruby remakes;

Out of the major studios left free, that leaves Retro Studios and Next Level, as I speculated above. Also a variety of smaller studios, probably working on download software (some of which could be already revealed projects), as well as spin offs. EDIT: Good-feel are developing Yoshi's Woolly World, not EAD Kyoto; presumably designers from EAD Kyoto are overseeing it, hence the Developer's Story from the Direct.

Turok is arguably the best 'mature' IP Nintendo could own and reboot. If done right,  it would offer something no other FPS seems to offer today. But that's just my opinion...

Pretty sure if a Megaman game gets made, it'd be made by Capcom - not Retro.

IDK if Nintendo really confirmed the existence of Pokken Fighters -- other than submitting trademarks here and there.

Mother 3 is probably the ultimate niche title. Seriously. We'll probably see X, SMTxFE, and a Golden Sun game all released before we see any movement on Mother 3.

Pokken Fighters will probably come at the annual Pokemon event around TGS-time, revealed to Japan first.

Either that or the game no longer exists.

There was a few seconds of video of a Wii U pokemon fighting game during some official Pokemon event, which I believe was paired with the Pokken Fighters trademark unofficially...

Also, I don't expect anything from Mother 3, but the tease was interesting....

where is pokken?
it really exists?

The 100 million was the purchase of some technology, mostly related to their QoL platform.

The other question is harder to answer because... well, let's face it, who would have said that Retro would be the ones doing Donkey Kong games?

With that in mind, they can be working on anything.

They alreadly made it, but was actually armature(former retro devs), and capcom alreadly cancelled that too: