They announced the Game to early. And the Failure of the Wii U made it even harder for Aonuma and his Team. So, yeah, they had to release Filler to close a giant gap between a new big Zelda.
It's not like Atlus is any faster with Persona 5 which was planned for a release in late 2014 until it got delayed, and delayed and delayed again to a release some time in 2016.