They should have made Animal Crossing amiibo do something cool in the game... or even just appear... if they wanted to clear those out.
There actually is some decent integration with the 3DS proper Animal Crossing game. But this was added after-the-fact, and did not come out alongside the release of the amiibo. Instead we got Happy Home Designer and a weak Wii U entry, both of which leaned more heavily toward supporting the cards. If we had gotten a proper Wii U Animal Crossing entry, the figures would probably be more popular.
Of course, it's only a matter of time before we see a Switch Animal Crossing game. The demand for those figures will likely bump when a proper Switch Animal Crossing title is released.