There's no point taking Iwata so literally. You've interpreted "it will take roughly a couple of years for us prepare new hardware" as "our next console will be launching in 22-24 months." He could just as easily be saying they won't be ready to show their next console until E3 2016.
The simple answer is that EAD Tokyo is currently working on their next 3D Mario game. It is most likely being developed on Wii U. (Even if it is intended for release on a different platform, there's no physical hardware for them to work with yet, and I believe Iwata said before that future Nintendo operating systems would be based on the Wii U's). So, when the time comes, the game can be released for Wii U, or for their next home console, or for their next handheld. They can just shift development to another platform.
Basically, no, games are not currently in development for Nintendo's next platform. However, there are games in development for Wii U now that will eventually be moved to said platform.
