We think it's fair to say that SEGA's acquisition of Atlus hasn't had a negative impact on the developer / publisher's output. Predominantly with RPGs but with other genres accommodated too, Atlus has maintained a steady release pattern of titles across various platforms. The 3DS saw some excellent releases in 2015, and there's hope that Nintendo systems in general could benefit from 2016 plans.
Atlus CEO Naoto Hiraoka was interviewed in the most recent issue of Weekly Famitsu, and he said the following when asked about plans for 2016.
In 2015, we were able to develop existing IP like Persona 4: Dancing All Night and Etrian Mystery Dungeon. In 2016, starting with Odin Sphere: Leifthrasir, we plan to release a large number of titles. In the summer, we'll launch the long-awaited Persona 5. Of course, in addition to that we have several unannounced titles. I have no doubt this will be a year Atlus' popular series all gather together.
While the release date hasn't been decided, I want you to also look forward to VanillaWare's 13 Sentinels: Aegis Rim.
Sony systems have arguably benefitted the most in recent times, so there'll be intrigue around Etrian Odyssey V in particular. Development is said to be nearly complete, yet there's still no real information of the game beyond some nice artwork on the official website and a teaser from late 2014. It's a series that's made its home on DS and 3DS, so there's natural curiosity over whether the 3DS will get the nod, a rival system - which would be somewhat controversial - or perhaps even the NX.
All will become clear, but it could be another enjoyable year for Atlus fans.