There's a lot of speculation going around that Nintendo just might buy Atlus. Although there has been no official statement from either company on the matter, some evidence of a close connection has lead fans to believe that this could be a very big possibility.
Most people are linking to the arguments from the International Digital Times article. As it points out, the developer has been making games for all three console companies, and in fact does a lot of good business with Playstation, but he focused on their recently cozy relationship with Nintendo. Atlus has done well with both niche Japanese RPGs (Shin Megami Tensei) and more casual games (Trauma Center) for the console, and they are currently doing heavy promotion for Shin Megami Tensei IV. More importantly, Nintendo has an investment with them for upcoming crossover Shin Megami Tensei IV x Fire Emblem.
The opinion piece ends by naming possible competitors to such a purchase, Sony being their biggest threat. Square Enix, Capcom, and Konami don't have enough reason to do so, and Western companies don't care. Overall, the piece seems to be highly speculatory in nature although it makes some good points.
However, there is more to this than the article suggested. It was revealed earlier this month that Nintendo is one of Atlus' biggest creditors, with Atlus owing them as much as 13,599,000 yen. They aren't the biggest creditor (that being Production IG at 44 million yen), however they do have incentive.
As we've seen in recent cases involving THQ and now Atari, Inc, in these bankruptcy proceedings, these companies were unable to complete initial sale to single buyers (albeit for different reasons) and were forced to sell their assets piecemeal. With Index acknowledging that Atlus is one of their most profitable assets, they have explicitly stated they intend to prioritize the company above others.
So, here's my own speculation. Index has incentive to approach Nintendo themselves first about buying the company directly, or possibly part of their assets. They could cover their tracks with Nintendo, possibly negotiate for debt forgiveness in return. Nintendo has also expressed interest in expanding their developer base recently, and actually did acquire Mobiclip. It's also possible that Atlus spins off into its own company, with Nintendo as one of its major stakeholders, with Production IG and others.
