Probably because they had to pay Capcom for the license to use Dante again.
Long LOST FACT.
Atlus in fact DID NOT pay Capcom to use Dante for SMT III in 2004.
The real story is Kazuma Kaneko did the character design for the Devil Trigger Forms for Devil May Cry 3 (Dante and Vergil) as a professional courtesy for Capcom and in return they allowed Atlus to use Dante in SMTIII.
Now you know. A story lost to the sands of time for the last 16 years.
mehh here we go again an original cut content for an extra money. no thank you greedy devs
Fees or not, cutting up content that was originally in the game to sell it to you again is not cool
There is no cut content as mentioned in RPGFlann's post above. There were 2 separate releases at retail of the game the Maniax version and then when Devil Summoner 2 was released it came as a LE with the SMT III: Chronicle edition.
Shin Megami Tensei III: Nocturne Maniax = Dante Version
Shin Megami Tensei III: Nocturne Maniax Chronicle Edition = Raidou Version
While it's not cool, they are in fact completely different builds of the game, so unless Atlus went and reengineered the game from scratch (and as a remaster, this isn't going to happen) you won't see them both in the game. (unless them make it so you can carry over data to the other version, but you won't have the story scenes play out in the same playthrough, THAT isn't a possibility)
I just think it's cool they brought him back, as far as the price, see my comments above. The original agreement was a gentlemen's agreement between both company's that everyone seems to have forgotten about (how shocking...) for work Atlus did for Capcom in exchange for the use of the character in their game to help boost sales. (remember a mainline SMT game hadn't been seen in Japan for years at that point, since the Super Famicom days, they were a re-releases on PS1 and other systems)
So that's why now they have to justify paying for it, since now they can't just do some character design for Capcom to justify the cost and call it professional courtesy.