That's not to say that it was a failure. As noted by Kimishima in the presentation, one of Nintendo's main goals is expanding into games for smart devices (phones and tablets), and Super Mario Run helped quite a bit with that endeavor. Ninety percent of downloads of the game came from outside Japan, and the game was able to enter markets that Nintendo doesn't have a traditional presence in with its console systems.
Additionally, it looks like the company will continue to improve Super Mario Run, rather than focus their efforts on developing a new Mario game. Kimishima said in his presentation that, "Our aim is for this application to be the definitive Mario application for smart devices." Despite the game not raking in what Nintendo considers acceptable profits, they claim to have learned quite a bit from developing the game that Nintendo will apply to future endeavors.
It's worth nothing that Nintendo's second mobile game Fire Emblem Heroes had a free-to-play model, rather than Super Mario Run's one-time fee. Of that game, which launched earlier this year, Kimishima said, "We are on track to meet our overall business objectives, including our profit objectives." It's probably not a coincidence, then, that Animal Crossing: Pocket Camp, which is launching next month, is also free to play.