Not even close, even if you don't count mobile/browser.
In the past two years, Atlus has developed or primary-published 9 titles in 5 IPs:
Dragon's Crown
Etrian Odyssey (4, Millennium Girl)
Persona (2 Eternal Punishment, 4 Golden, Arena, Arena 2)
Shin Megami Tensei 4
Soul Hackers
And published Conception 2, Game of Thrones, Aquapazza, and Testament of Sherlock Holmes in the US.
Counting mobile, you can add Knights of the Sky, Shadowland, and BattleSpace.
For Square, you've got 26 in 13 IPs:
Bravely Default (BD:FF, BD:FtS)
Deus Ex HR
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C
Drakengard 3
Dragon Quest (VII, X1.0, X2.0, M:TW)
Hitman Absolution
Gunslinger Stratos
Gyrozetter (arcade, WoA)
Final Fantasy (III, VII PC, VIII PC, X:HD, X-2:HD, XI:SoA, LR:XIII, XIV:ARR)
Kingdom Hearts (1.5R, 3D)
Quantum Conundrum
Sleeping Dogs
Theatrythm
Tomb Raider
And published in Japan: Call of Duty (BOII, Declassified, Ghosts).
Counting mobile: DQ, DQ8, FFXIV:TAY, Pictlogica, FFII, FFIII, FFIV, FFV, Star Ocean MT, Guardian Cross, YIS Million Arthur, Chaos Rings, Line Neko Jump, Line Slime Gozenitor, FF Tactics S, TWEWY Live Remix, FF ATB, Circle of Mana, Chaos Rings 2, Seiso Dragnir, FFT War of the Lions, Chocobo Farm, FF Artniks, Demons' Score, Emperors SaGa, Otome-Break, Nirvana of Genesis, FF Legends, KSS Million Arthor, Lord of Vermillion 774 Deaths, Chaos Rings Omega, Itadaki Street, FF Brigade, Occult Maiden, Melpharia March, Bloodmasque, Sangokushi Renbu, Crystal Defenders Plus, Theatrythm, Symphonica, TWEWY Solo, DQ: Monster Parade, Kingdom Hearts Key, Thousand Heroes, Star Galaxy, Legend World, BD
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B, and Crystal Conquest.