In an interview with Famitsu, Persona Q: Shadow of the Labyrinth chief producer Katsura Hashino explained how the 3DS game came to be.
It all started with an interest in working on a new collaboration title following Persona 4 Arena. Hashino said they were aware of fans who had hoped to see the Persona series on 3DS and “felt the need to respond to that”.
Hashino’s comments in full:
“We were able to make the series’ first fighting game with Persona 4 Arena in collaboration with the folks at Arc System Works, and we also felt the desire to work on another fun collaboration. …while we were making Etrian Odyssey games and many other Atlus games for the 3DS, [we were reminded about] all the voices from fans who’ve been wanting to see a new game from the Persona series for the 3DS, and we felt the need to respond to that, and that’s how the plans of a collaboration within Atlus came to be.”