Like Team Galactic's Commanders followed a planetary naming scheme, the Rocket Executives are all named for various real-world rockets. Rocket Executives are also redesigned from Generation II, with four new ones appearing: Archer, Arianna, Petrel, and Proton.Team Rocket Grunts are redesigned once again.Some of these images change depending on the time of day while others change the image of the Pokémon obtainable at the location on the image at random. An image of certain locations, like in FireRed and LeafGreen, appears when entering the location.Unlike Kanto's remakes, which contained the same regional Pokédex as the originals, the original regional Pokédex for Johto has been slightly altered, including several Generation IV evolutions for Pokémon found in Johto. Much like Kanto's was for its remakes, Johto's Pokédex has been redesigned.There are a range of skins that can be used and changed at the player's will.

A GB Soundskey item allows the player to switch back and forth freely between the arranged soundtrack and original chiptune soundtrack. All the game's music is rearranged to better utilize the DS's sound capabilities.The male player character receives a redesign and is now called Ethan, while Kris is replaced by a new female player character called Lyra.

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