Atlus USA has been going down the toilet since 2009 or so.

While other niche companies like XSEED have been working on localizing games that they're passionate about and want other people to play, ever since they succeeded with Demon's Souls it feels like they've been more focused on publishing console/digital ports of western games that they don't have to do any actual work on to turn a quick buck in hopes of cashing in again on the portion of the Souls fanbase that hate anything that looks remotely japanese. Even if the titles aren't all that great or no one particularly asked for them (hi Cursed Crusade). ...though, they've always been a bit aloof and distant from their fanbase and their suggestions (at least XSEED is reasonably transparent if they don't want to or can't bring out a game). And to be fair they're bringing out Dragon Crown which a lot of people have been wanting for a long time (despite my not knowing why, since Vanillaware is a shitty company that focuses on appearance over actual substance aside from the big two reasons lol). Furthermore their translations have felt a bit sloppier lately (with a lot more text clipping out of the box or leftover html tags), and they've gotten away with cutting out content from games without anyone noticing. At least they're still good about reprinting their more sought after games when sequels come out.

Atlus Japan still makes good games, but they've (well, Index) been milking their intellectual like crazy recently because of Index's financial trouble. Like all the anime tie ins or the 2 year turn around on releasing enhanced ports of the Devil Survivor games.

Sadly it feels that anymore no one cares Atlus beyond Demon's Souls and P3/4. :(

a lot of companies are shutting down, i will laugh if they blame it on indie

Well, at least it looks like Shin Megami Tensei IV will still be releasing in two weeks.

Atlus has built up a pretty strong reputation with the SMT series, I'm sure things will end up ok for them.

More like the Japanese governments' currency weakening policy

That's designed to bolster companies that deal with export markets. The J-government doesn't give a shite about the domestic market or domestic consumers. As I've said before, they want domestic prices (which are already exorbitant) to increase further and to continue increasing.

As for whether Atlus will become independent? That depends on whether they can afford to buy themselves out from under Index I would expect.

http://www.latintimes.com/articles/6597/20130722/atlus-bankruptcy-nintendo-2013-index-corporation-tensai.htm
It appears likely that Atlus will be purchased by NIntendo. I take it, such a fate would mean that all future Atlus games would be Nintendo exclusives?

owwh, that hurts. Bad news for Persona 5.
Atlus is one my fav developers, maybe there is still hope that Sony gets the deal.

Don't put that much faith into that. Reading the source article you'll see it's nothing but speculation on the part of the writer.

Nintendo tends to work closely with companies releasing exclusives on their platforms, especially high-profile ones. Atlus' case isn't special.

As for those releases being exclusives on the first place, there's a much simpler explanation: money. Atlus isn't that big of a company, that's why they kept releasing games for the PS2 long after the PS3 was out, it was cheaper to produce and had a big enough install base; it's also the reason for all their DS games, and for having made only a single game for HD consoles, Catherine, during the entirety of this 8 year long generation.

Looking at the current platforms though, what do we have: the fading past generation of HD consoles, the coming next-generation (and the Wii-U in the middle), the Vita with its low-install base and high-production costs, and the 3DS, far and away the least powerful, though cheapest to produce for, of them all.

Finally, we have Iwata who has made it his mission statement to bring in an operating profit of 100 billion Yen over this financial year, around $1 billion. Atlus, as a company separate from Index, has been valued at around $150 million. Since the Wii-U hasn't exactly been setting the sales charts on fire lately, I'm not sure they can quite spare the money and still meet their goal.

Of course, I could be wrong about all this, Nintendo could see an opportunity here and go for it, money be damned, but gamers have a very limited view of things; we forget that Nintendo and Sony aren't the only two companies in the world that could buy them. Atlus made money, Index failed due to their own shortcomings, another big corporation might very well buy them and take Index's place which, frankly, is the best possible scenario.

Interesting. It sounds like a good business decision for Nintendo, as I think they could use some fresh franchises/IP. As an Atlus fan, possibly my only concern would be some of Atlus' somewhat darker and more mature themed games being "nerfed" down to appeal to a broader audience. Time will tell.

But Persona already exists, and that's on a Sony platform.

*shrugs*

If Nintendo buys Atlus then that means every game that Atlus has ever released on a non-Nintendo platform would never see another release again.

So you damn better hope they don't buy them.

Counterpoint: Soul Hackers.

Though yeah in the short term stuff might get removed from PSN/XBL in such an instance

That's an exception because Soul Hackers -was a port-.

Atlus published a lot of different games on various systems. Anything on PSN / XBL / Steam would be removed solely because Nintendo will never release any of their games on a competitor's service. Period.