According to the development team in the game's official Japanese guide book, during the planning stage they had a list of dinosaur names they wanted to include the game. Two dinosaurs that were on the list but left out of the final game are Triceratops and Ankylosaurus.
Contributed by ProtoSnake
According to the Capcom team in the game's official Japanese guide book, they were asked about the meaning behind the name of Ibis island, and they responded:

"The name of the ibis bird in Japanese is “toki” (a homonym for time), and we liked how that word resonated with the game’s themes of “extinction” and “time”… we could probably come up with a number of different explanations for the name, but basically we liked those associations. Also, considering the name of “Raccoon City” from Resident Evil, maybe there’s a lot of animal lovers on the team too."
Contributed by ProtoSnake
The number of continues is much greater in the Japanese version compared to all other regional releases. Japanese players are granted 30 Continues while all other versions only have 5.
Contributed by Regen-33
In the Japanese PlayStation version, Regina's Inventory Menu portrait is different from the one seen in other releases.
Contributed by ProtoSnake