New Super Mario 3DS, Zelda and Pikmin games are in development but Shigeru Miyamoto is focusing on finding the next big hit rather than working on Nintendo's big franchises.

"After all, developing big hit titles must be the solution," he told investors. "I am acting with the understanding that one big hit title can change multiple phases of a situation in the entertainment business, and I feel that finding such one big hit is my basic job."
Last year, Miyamoto said that he hopes to reveal a new game within a year. Will this be his next big thing? We'll have to wait and see.
[ Source: Nintendo ]

It will be a six dimensional platformer controlled almost entirely with the gyro.
A new IP is never a bad thing.
Though I must say, we're well overdue for a new F-Zero....
I'm sure whatever he comes up with, it will be great anyway.
I welcome new and fresh ideas and look forward to hearing more...
However if Miyamoto focused on that they've built upon, i'd like to see:
-More Yoshi/Diddy Kong/Banjo/Wario
-De Blob 3
-Please please please, a 3d remake of the gbc Reservoir Rat
-Toon Link 3ds
-How about a Mushroom Kingdom detective game along the lines of Scooby Doo/Mystery Inc
Here you could have:
Mario and gang visiting various Mario or Ninty game worlds/universe, with Luigi's Mansion 2 (or Monster Hunter even) explorations in terms of haunted mansions, shipwrecks, beaches, caves, jungles, mountains etc and solving puzzles and clues like the Prof Layton series...
Or
a Mario and crew (Luigi, Toad, Wario, Yoshi, Bowser, Donkey Kong etc) game featuring two sides to the story similar to Lego Batman with Hero and Villians
Or
Super Mario 64/ds, Galaxy 1 and 2, Sunshine etc rolled into one...
Wouldn't be more confident of anyone saying that than I am of Miyamoto-San, complete legend and genius, really looking forward to what he come up with!
A couple of them don't make sense - De Blob isn't made by Nintendo. You get confused that Nintendo develop first party titles and other developers outside of Nintendo make other third party games. I don't want to see Toon Link on 3DS, there's been too many DS games for that and they've made clear that it won't be part of the Toon Link saga. I think they'll work off of the Ocarina of Time 3D engine and change it up, like they did with The Wind Waker, when they turned that graphical engine into Twilight Princess (hence why Twilight Princess used soundbytes from the Wind Waker).
I think the best way of going about it would be to somehow invent a new genre rather than attempting to re-invent.
Also, I expect the subject matter to be something that Miyamoto is passionate about outside of gaming. It was his childhood love of exploring caves in his hometown that led to Zelda, and his love of dogs that made him come up with Nintendogs. Two very games but both big sellers. If Miyamoto can do what he's alway done, making games that he likes, then I'm sure that hit will come to him.