Coming from a Game Informer interview with producer Eiji Aonuma...
“The dev pace is not really dependent on how many people are on a team, so combining them would not necessarily expedite the development pace. The 3DS team and the Wii U team have different approaches to game development, so I don’t necessarily want to combine them and have them think together, but rather have each think about what they can bring to Nintendo Switch from their own perspective.
The handheld development team will not be phased out because of Nintendo Switch. Switch will allow the users to bring their home console on the go, but this doesn't mean handheld game development like Nintendo 3DS will be discontinued. Yes, there is definitely a possibility (that 3DS Zelda team is working on a Switch title).
There are definitely good things about the 2D world and the playstyles of the 2D world. There are a lot of fans who enjoy that style. This Nintendo Switch style, which is the evolved style of gameplay is not necessarily… I want you to think of it more as an evolved style of 2D style. For the 3DS team, I am trying to make them think in a more evolved 2D-style approach"