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Have the 2D Zelda guys work in it, and develop a new engine for the console after the Switch.

Maybe Animal Crossing, or some smaller spin off titles will use the same engine.
Nintendo will probably merge the more successful tools they developed with BotW into their toolkit, and retire the rest of the engine.

The Switch is a new piece of hardware, with a very different hardware architecture, new methods of rendering scenes will be looked at.

Also I think they were talking about the Zelda formula in general.
I would bet that a big portion of the development time with BotW was spent figuring out what type of a game they were making.
BotW is a very experimental game, new understandings of game design was the true value gained.