It's sad enough that SMT was on 3DS and got dumbed down significantly in scope compared to its PS2 brethren. NEVER AGAIN
Except for SMTV and more megaten games on the 3DS for sure over the next 4 years or so

SMTIV sold really well!
I'm perfectly fine with the way Atlus is/was setup last time I checked:
Persona team -> console big budget Persona games -> P5
Handheld team -> SMT SJ/SMTIV type stuff -> ?
EO team -> EOs -> Persona Q
Port team -> port port port -> ?
Growlanser team -> Devil Survivor 1 & 2 -> FE x SMT?
Not sure what happened to the Trauma Team staff, but I have a feeling when P5 development went full gear they got pulled into P5 team. Also with how incredibly successful Catherine was, you would have thought they would've hired more staff and branched off another team to make a Catherine 2 by now, but who knows.
It's a pretty solid and smart spread of staff that gets a lot of different budget, different quality, all still good products. Hopefully the whole Index bankruptcy -> Sega buying them isn't going to fuck this stuff up although it appears it already had an effect on P5. Hopefully that was just because of the transitioning between companies and now everything else is back on track.
And once the P5 team finishes and they have a new set of 3d demon models to use, I expect them to take some chances on new IPs again like how Digital Devil Saga, Devil Summoner (yeah I know not a new IP, but might as well have been) did on PS2.