There isn't much marginal benefit in Nintendo buying Atlus.

[Otakumegane]

kupomogli said:

To Nintendo, yes, but to other developers no.  The Fire Emblem games were never a shining example of graphical prowess.  The fact that every GBA game is graphically the same while all the DS have the same animations and only look a bit better proves that.  Expect to see Fire Emblem Awakening graphics on the next five games in the series.

Atlus games are much larger in budget than the Fire Emblem games and the sales are worse.  Whether these sales are correct or not, it's currently showing seven different Fire Emblem games above 500,000 sales, with two of them selling 970,000.  Fire Emblem Awakening will pass a million sales eventually.  Compare this to any Atlus "developed," not published,  game and there's only five which sold over 500,000, two of which are remakes/rereleases(Persona 3 FES and Persona 3 Portable.)  The highest selling game is Persona 4 on the PS2 with 820,000.

If you want some more comparisons, their highest selling DS title is Trauma Center with 340,000.  Highest selling RPG is Etrian Odyssey with 300,000.  Highest selling SMT/spinoff is Devil Survivor with 280,000.  SMT4 sales at 250,000 are their highest 3DS sales(which I believe should pass 400,000.)  

Rarely does Nintendo put any sort of massive budget towards their franchises.  Titles they can't get away without putting a decent budget that happens not to sell as well as they hope gets ignored for a very long time.  Metroid Prime The Other M anyone.  Sells well over a million copies, only for Nintendo to come out and say they were disappointed with the sales.  When has been the last time we've heard anything about a new Metroid other than fan made works? 

If Nintendo bought  Atlus we'd see maybe one or two games a generation.

I'd like to see some good reasons why you think this. If anything, I'm playing SMTIV right now, and while the game's good I keep thinking it lacks a certain degree of polish in the presentation (Argh those sprites are so jarring with the artstyle they chose to represent it in). Cutscenes aren't even animated.