A lot of you are confusing Atlus-published with Atlus-developed. Broque and Gungnir are Sting. Unicorn, Sentinels, Dragon and Princess Crown, and Odin are Vanillaware. 7th Dragon and Stella Glow are Imgeepoch (may they rest in peas). Dodonpachi is Cave. They published a lot of really solid games, I'll admit.
If we're going off best, I'd say Etrian Odyssey III, or Shin Megami Tensei: Strange Journey. EO3 has probably the best classes to play with (beyond Hexer), and SJ feels more like a perfect SMT game than what came before and after, on top of having mechanics that are just weirdly absent from later games (such as enemy demons noticing if you're lugging a corpse of their species around). If we're going off my personal favourites, I like the jank of Trauma Center DS and Etrian Odyssey I to the point they endear me more than their better made sequels. Devil Survivor 2: Record Breaker is easily the best of the 3DS era, owing in part to the god tier voice acting on top of what's already a great game. Trauma Team is great, aside from the endoscopy stuff. Shin Megami Tensei 1 also holds up incredibly well, having first played it last year. Just play the PS1 version.