Okay, now that it's not O'dark-thirty in the morning, I can elaborate on what I'm worried about.
Frankly, I don't see anything bad happening with Atlus of Japan, hell they might use some of the talent to make like a Growlanser/Shining Force hybrid or something, which is all very well and good. No, my problem is in regards to Atlus USA's fate since Sega's been like, really really bad about bothering to localize any of their RPGs as of late (they'll no doubt continue distributing Sonic and stuffs like Vitrua Fighter, provided they still do that). Anyways, since the majority of Atlus' output is RPG based, I suspect one of two things happen A) Sega gets smart for once and actually have Atlus USA localize some of their RPG titles that have otherwise been stranded in Japan as well as letting them continue work on their own stuffs unabated, or B) Sega does the usual and continue to not bother letting any of their RPG content see the light of day outside of Japan despite whatever interests or infrastructure might exist and forces Atlus to shut their USA branch down as a cost saving measure (since without the RPGs what do they localize?).