Conception 2 is only an Atlus game in the west. It was funded, developed and published by Spike Chunsoft in Japan. If you include their localizations and western indie games, Atlus' Vita lineup isn't as bad, but not something really worth noting. From Atlus JP, it's still Dragon's Crown and P4G.
I'd be surprised if SMTxFE is mostly developed by Atlus and not Intelligent Systems. If they're so strapped for staff, they shouldn't be devoting them to platforms like Wii U. While I know I'm advocating them making games on a platform no better in sales, at least you'll be able to count the total amount of RPGs on Vita with more than one hand.
While 3DS2 was hilariously delayed, it's not like their lineup on the platform completely fell apart.
If that were true, DAN would've likely already been released by now. There's a reason why Atlus has taken development internal.
I dunno, Atlus in general relies on ports or reused assets to make new games, (not that I hate them).
On the 3DS if you take away the ports and games where Atlus only serves as the publisher you would have SMT IV and EO4 and PQ. As least that's what I can think of. Catherine is the only game I can think of that's made by Atlus JP on ps360, Arena/Ultimax is a joint project where ArcSys does the work.
The vita is in an odd place for ports, since idealistically it should receive a port for Nocturne and the DDS games and PSP ate up all the other ports for older games (and it would require tons of work to make it look nice on the Vita), or the Raidou games, but I don't think they are going to work on them. I would love for a port of Nocturne though, but it's not going to happen.
^This kinda reminds me of the Extra Credits EP on why Vita is struggling, a bit too ahead in terms of power for devs to budget for a handheld game.
What I'm saying is that Atlus relies heavily on ports and publishing to make buff up their line ups, their output reduced drastically since PS3/360 took over, Vita doesn't have as much ports as 3DS did, coupling the fact that Vita is selling like shit outside of Japan it's not going to help.
I do agree with you on DAN though, I think you have a good point now that you mentioned it.