The idea here is to release a piece of hardware that enables Nintendo to release games that aren't bound by the usual smartphone games "guidelines" that every game developer has to follow when they enter the software development environment of mobile games. This is obviously an assumption, but I think it's a safe one.
I game on my smartphone but I choose my games carefully, turn-based RPGs, for example, work really well on smartphones. Try to make a platformer like Mario and you will end up with a bad game. What if Nintendo wants to offer that kind of experience on the iPhone? A controller add-on can be the missing key.
Nintendo is still testing the waters with mobile games, we'll see what will happen if they decide they want to continue to be in that market.