In an interview with Famitsu, Miyamoto hints on the brand new Nintendo franchise he has been working on. He states that it has been keeping him busy, but won't provide more details.
In the same interview, Miyamoto also elaborated on some design choices for Super Mario 3D Land. They did decide to add Princess Peach after fan demand for a playable female character, and recognized that women would not necessarily prefer to play as either of the plumbers. He then adds that using Peach's floating ability, as demonstrated in older platformers with her, would make her an ideal character for beginners to play.
In spite of this change, Miyamoto stresses that Nintendo does not intend to stray too far from some core Mario game design elements. He particularly points out that many other games will let the camera move around, and although gamers enjoy these games, they're often unable to work out what they're doing. Miyamoto says they want Mario gamers to always be able to consciously plan out their course of action.
Lastly, Miyamoto believes the Wii U's latest update has positioned it to the point where it's convenient to use in the living room, and pledges even more improvements in the near future.
MIyamoto has been dropping hints on the mystery new IP since last year. However, Nintendo has been better at keeping their secrets than most, so we simply have nothing to go on when it comes to this new IP. He's also expressed an interest in making a first person perspective game before seeing the popularity of FPS games, although he may not be making a shooter.