I don't think there will be one system replacing both the Wii U and 3DS. How should that work? Home consoles and handhelds have distinctive features and people buy them for different reasons. You can't have a concept like motion control on a handheld and dual screens don't work on home consoles (which the Wii U proved). I think Nintendo's future will feature 3 "platforms" to release their games on:
- Home console with something like motion control and multiple controllers (maybe sensors? Sensors will be huge)
- Handheld with touch capabilities (and again: Sensors are a possibility)
- Games for smart devices, distributed via App Store
--> All of this will be tied together via one single membership service. Some games will be relased for handheld + smartphone. Others for home console + handheld, etc. You'll be able to keep your games across platforms and play them on different systems as long as the controls allow for that. You'll only have to buy a Virtual Console game once.
The home console and handheld will feature similar architecture. This is exactly what Iwata said multiple times. He never mentioned a "fusion" concept, but he did talk about this. The home console will be more powerful but they'll share the same fundamentals. This will make it easy to release games across platforms *if it makes economic sense for a title*. Mario Kart could feature tracks, music, assets and other things that will be used in both versions but the home console version will run at 1080p and not all tracks and drivers will be the same.
Nintendo will also need less time to get accustomed to their new consoles as they'll only have to learn to program in one environment instead of two. Porting games across platforms will be easier. Virtual Console titles (and lots of eShop games) will be released for both platforms simultaneously. Maybe cross-platform online play will be possible for some titles.
I don't think we'll see a "fusion console" as in one piece of hardware that acts as console and handheld. It would satisfy neither market and fail spectacularly.
