Looking at the list of recent Atlus games, out of their big name franchises, it appears that only Persona wasn't on a Nintendo console. In fact, Nintendo even has some exclusive Atlus franchises like Etrian Odyssey and Trauma Centre. It's only standalone games like Catherine that didn't make it, it seems.
However, what is interesting though is that Nintendo recently trademarked the "Fire Emblem" name, despite the franchise trademarks not expiring any time soon. One possible guess is that development of Shin Megami Tensei x Fire Emblem went haywire, so Intelligent Systems are now using the Fire Emblem assets they had already made for that game and making a standalone Fire Emblem game - after all, there's no way they could be working on another 3DS game so soon after Fire Emblem: Awakening and working on two Wii U games at once would be madness.