I would have to say either Splatoon or Mario Maker. Both of those games really showcased what Nintendo was capable of when they are motivated to perform at their best and not just sit back and enjoy their financial success (BotW did this too). That said, these two games specifically were created to compete in completely new genres for Nintendo and the genres were already really well-established (level creation and online shooter). Not only did Nintendo make decent installments in both genres but they actually made enormous waves.
Splatoon was just a brilliant game and is a perfect example how a small, inexperienced team of developers can change an industry when they are given the freedom to take risks and follow their imagination. Most FPS's today have such massive budgets and focus on ultra-real graphics to the point that no developers want to take any chances experimenting with the fundamental game mechanics, anymore. Nintendo did exactly this with Splatoon and it paid off massively.
Mario Maker was the game that finally found the perfect use for the Wii U gamepad. Unfortunately, it was too late in the lifecycle of the Wii U to change its fortunes, but if Nintendo had been using their brain when they launched the Wii U they would have seen that level creation was really the one big thing that can justify the existence of the gamepad. Mario Maker was the best utilization for the gamepad and something that no other game console can do as well as the Wii U did. Nintendo, should have been integrating level creation aspects into all of their first party titles in a way that it was an integral part of the game design (like they did with motion controls on the Wii). I think that if this had been done, the Wii U might have been less of a disaster as developers would have had an idea of what to do with it.







