First off, I'd take this article with a grain of salt, since they almost outright state that Nintendo wants to buy them; I think that's sensationalist journalism just to get hits. I highly doubt Nintendo wants to buy Atlus; it's not like a niche publisher like that would sell the Wii U or the 3DS, even as popular as Atlus is. They may express interest in acquiring Atlus, but at the price point that Atlus of Japan is expected to sell at, Nintendo would likely take a pass unless they could get Atlus on the cheap.
Of course, if Atlus of Japan folds, it does put the SMT x Fire Emblem project in jeopardy.
Best-case scenario I see is if another niche publisher merges with Atlus and helps with distribution rights (especially in Europe, since Atlus has no presence there), and Atlus stays third-party as usual. Gungho (which I think has Acquire and Grasshopper under their belt) or Marvelous Entertainment (which is in bed with XSeed) would be the best fit for Atlus, but they may not have the capital to afford Atlus. Nippon Ichi is also a possibility, considering the two companies have a good working relationship with each other, but NIS has been struggling as of late (especially now that they've lost the Atelier series' publishing rights to Tecmo Koei). I highly doubt Sony cares about Atlus at this point; they didn't exactly treat Atlus well regarding the current gen, and Atlus doesn't sell enough units to make it worth their while. I can't see Microsoft or any of the bigger western publishers expressing interest at all, and a Squeenix, Capcom, Konami, or Bamco merger would likely be disasterous, since they'd likely get kicked to the curb like Microsoft's done with Rare these days.
But this is all speculation at best until a deal gets done (or not), which likely will happen around September, hopefully before TGS so Atlus of Japan can focus on that. Otherwise, I'm not touting any gloom-and-doom scenarios until then.
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