Soundwave on 19 January 2017
My read on this is I think like for games like Splatoon 2 you'll be able to play online just the same way the Wii U does (no app needed).
BUT if you want to do the matchmaking, playing with friends, playing with voice chat stuff ... all that is going to have to be done through the smartphone app.
This is one way Nintendo is keeping kids from playing with "strangers" as younger kids will likely be forced to have to use their parents phone, and then their parents will be able to see who they're playing with.
