This is just a little poll to see who everyone prefers. I didn't want to include Square-Enix because while I feel they make great games, I don't feel they innovate very much. Both Atlus and Nippon Ichi have similar goals, with Atlus innovating turn based RPGs and Nippon Ichi innovating turn based strategy RPGs. You make the pick. Here's a list to brush up on from the PS2 era to today:
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Developed by Atlus:
SMT: Persona series
SMT: Devil Summoner
SMT: Digital Devil Saga 1 & 2
SMT: Nocturne
Growlancer series
Bonus*Trauma Center series
Bonus*Maken X
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Developed by Nippon Ichi Software:
Disgaea series
La Pucelle: Tactics
Makai Kingdom
Phantom Brave
Soul Nomad & the World Eaters
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I personally think Nippon Ichi makes better RPGs, but not by much. Disgaea is like crack to me, and I'm really enjoying Soul Nomad & the World Eaters. Both have a great quality and each developer has a true identity you can see passed through to each of their games. I find Nippon Ichi to have more humorous storylines while Atlus takes a more controversial approach which is also real nice. So discuss who you like better and why.