The earlier games were all works of Cozy/Kaneko along with the writer Satomi Tadashi (who self inserts himself in Persona 1 and in P2 marries his waifu Tammy, the heroine from SMT If).
Cozy left after Nocturne to do some bad PSP games at his own company
Gaia and later headed up Cave Online which made SMT Imagine - looking it up, seems like he's just been making mobile games since then.
Tadashi last worked on the scenario of DDS along with the novelist Yu Godai. He seems to have left the company since then?
Kaneko last did character/world design on DDS, directed/wrote/did everything on the Raidou games, character designs and concept for Strange Journey, and did the original concept/rough scenarios for SMT IV. I think he's slowly retiring and letting the next generation of Atlus take over the reigns? Though, when I asked some buddies at Atlus about it, they said he's still around and doing stuff so who knows? Probably a lot of the behind the scenes stuff, or maybe he's just become fully management at this point and is thoroughly entrenched in office politics and trying to keep the company afloat.
Either way, I agree that Atlus games have lost a lot of their appeal without Kaneko. I think Hashino is a great director and every game he's touched has been fantastic and better than the last, and Soejima is a fantastic designer and his stuff is amazing - but what got me into Megaten was the vibe of creepy occult + oppressive atmosphere and the slick, eerie designs of the characters, which is really missing from the modern era.
SMT IV was a great return to form with its harsh atmosphere and twists on the series tropes. I hope they make more like it. Likewise, Devil Survivor has a great gameplay system but I really wish the character designs were Kaneko instead.
Hell, if they just offered a DLC skin that'd redraw all the characters in every new Atlus game in Kaneko style, I'd be the first to buy that shit and play through every game. As it is, I have trouble getting through all these P4 spinoffs and Devil Survivor remakes.
That said, I'd rather play any Atlus JRPG than any other JRPG out there. I'll probably play through and really enjoy SMT x FE despite how much I dislike how it looks.
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THAT SAID,
here's a survey Black and I were running about SMT acrylic character keychains we wanted to make!
Vote for the ones you'd buy and we'll make 'em! Though the votes are waaaaay over now and we've already decided the 34 we're making, but maybe the 5 votes of whoever reads this thread will be enough to push someone back into the ranking?