In light of Iwata's comments about showing various internally developed games for Wii U that are at various stages of development at this E3, I thought I'd take a stab at who some of the directors might be. I'm not saying that each of these groups has a game in development, or that it will be shown, I'm merely speculating.
-Animal Crossing U: Neither Director on New Leaf has been on any other projects, as far as we know and the Animal Crossing Plaza is designed to end at the end of this year. I don't think anyone from Monolith Kyoto was credited for Mario Kart 8, so I think it's likely that team is assisting with Animal Crossing U and/or Zelda U.
-Zelda U: Already confirmed to be there in some form. I imagine it'll be directed by Hidemaro Fujibayashi, as was Skyward Sword. I imagine Monolith Kyoto is assisting with design elements, as they did on ALBW.
-Hypothetical Yoshikazu Yamashita & Takayuki Shimamura Project: The co-directors of Wii Sports, Wii Sports Resort, and Nintendo Land. While Shimamura has been overseeing the Wii Sports Club development, I don't believe that's all he has been working on. With Iwata comments about showing games that make use of the Game Pad, I can't imagine the inevitable project these two are working on doesn't get shown after a little over 18 months development, even if they typically have ~3 years between their games. They are the proverbial kings of making use of the controller gimmicks, after all.
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Hypothetical Shigeyuki Asuke Project: This guy directed NSMB and NSMB Wii and then was only responsible for planning on NSMBU and didn't touch NSMB2. Being responsible for 2 of the best selling games on the Wii & DS, I think he's been given a new project; possibly the primary NFP one.
-Hypothetical Yusuke Amano Project: First project as a director was NSMB2. I not sure about this one, but I think there's a possibility he's been given another project to work on. Only mentioning because it'll be nearly 2 years by E3 since NSMB2 launched.
Hypothetical Daisuke Tsujimura Project: Works in Tokyo EAD and worked on Galaxy 1+2 and 3D Land as a planner/planning director, but is conspicuously absent from 3D World's credits. This feels like an unlikely thing because he may have moved departments or left Nintendo entirely. If it does exist, I have a feeling that it would be primarily developed by a 3rd party.
-Kouichi Kawamoto: A bit of a wild card for me but he was the guy who created the WarioWare prototype and designed the Mii Plaza/Find Mii.
Mr. Miyamoto said back in 2012 that he was a 'a very strong figure [who] will play a very important role in the future.' Regardless, I do think, though, that he's likely deeply involved in either QOL or NFP.