Are you sure about that?
Dragon Quest XI sold 1,72 milion, Monster Hunter XX sold 1,61 million, both were launched this year. And Pokemon Sun/Moon sold more than 02 million copies this year too (12+ millions in 2016). There are still two potential millions sellers: Metroid and Pokemon Ultra Sun/Moon. The 3ds year may still end with 05 or even 06 million sellers, if Fire Emblem Warriors also sell well (something that I doubt).
Still, it´s true that although this year has been great for the 3ds in terms of quality, most of the games did not got so much attention from its owners. I belive that the reasons are: 1 - Few main titles from the most popular franchises (too many spin-offs) and 2 - the huge hype around the Switch.