This is the first mainline Shin Megami Tensei game not to feature moon phases or some variation thereof.
Bad Export for You: The game's European release came well over a year after the Japanese and North American ones. It was in English only, in contrast to the standard of European-release games being available in multiple languages, and was available only for digital download, unlike the Japanese and North American releases which are both available in physical form as well.
Same goes for the players living in Central America or South America. For some unexplained reason, these were region-locked from acquiring the game via Eshop. Importing a physical copy was the solution for these, if expensive, but it still would keep those players locked from acquiring the DLC all the same, leaving them with an incomplete game in comparison to other countries.
Thankfully averted since the release of the sequel, which, in order to bolster interest on its sales, lifted the region lock from these countries. Three years later, yes, but hey.
Troubled Production: While a more subdued case than most, the game suffered from the new and old members of Team Maniacs having different ideas of what to do with the game causing a drift between them, with the old guard wanting to stick to series standards while the new wanted to input things they where accustomed to such as "sweet" female characters and various classic anime tropes.
The standard Samurai uniforms used to be gray and black until they decided that it wouldn't make sense for the Black Samurai to be considered conspicuous if all Samurai wore dark uniforms so they switched to blue and white.
The audience room of Mikado Castle was cut as a visitable location because of how little importance the king ended up having in the game itself.
Lucifer Palace and Purgatorium were originally the final dungeons for the opposite alignment route, Lucifer Palace for the Chaos route and Purgatorium for the Law route, they were switched for symbolism.
An idea that went unused for Lucifer Palace was Lucifer's eye being seen in windows, watching the party as they make their way through the dungeon.
Akihabara was originally going to be explorable before being cut entirely. It's explained in-universe as the Ashura-Kai destroying the ward in what appeared to be a military strike.
Reverse Hills had some content that was too graphic for a Cero C rating, so they toned it down.
The designer of Chemtrail, Tamotsu Shinohara, had initially wanted to put Illuminati symbolism in its design as part of its conspiracy theory aspect, like a one eyed pyramid imprinted on its stomach, before deciding that it might cause problems later and scrapped the idea.
According to the Megaten Maniax book, the original script Kaneko had created for the game was so massive, it is described to have been able to fill upwards of 7 to 8 volumes of Japanese novels. Supposedly it was split into two huge parts internally called the Resurrection arc and the Destruction arc. The game is mostly based on the content in the Resurrection arc, while the material of the Destruction arc mostly went unused.