What will happen to Atlus now that SEGA's in their current situation? Will they be fine or suffer greatly?
Given that Atlus just announced Persona 5, I wouldn’t worry too much about them.
Sega does not technically own Atlus, anyway. Remember, this is how things look:
Sega-Sammy is the mothership entity here — it handles pachinko and other arcade-related stuff, as well as managing the overall company. The actual stand-alone “Sega” branch, the part that is in trouble, is technically separate from Atlus.
If Sega shrivels up and dies, it shouldn’t have too much impact on Atlus, outside of maybe Sega-Sammy pressuring them more to succeed and make up for Sega’s loss.
It’s kind of confusing, I know, but as long as you keep in mind that Sega and “Sega-Sammy” are technically separate entities, it makes a lot more sense.