The most important thing is to see if the console can handle Wii and WiiU software one damn way or another. I don't believe it won't be through ports though, it takes quite a lot of time even for a single game.
For controllers I believe is no big deal, they made that Gamecube pad adapter, so they can make it through eveything. You'll only need the right device or just minor hardware updates via Internet download (the 3DS connection app as another controller for Smash WiiU). But if they don't let the older games be playable in this new console from, at least, the previous generation ... they'd simply loose a quite big deal of oportunity for those who didn't buy WiiU. More games for them plus the new ones for NS' release, which will be around ten, but possibly no much more than that.
I do seriously doubt they would buy a console that they never had any kind of interest since many years, to begin with, so ...