The game is set in Hoenn as before, but with differences and new places.
The characters are the same as in Ruby and Sapphire, but they have new clothes (some parts, such as Brendan's headband and May's bandana, have been colored green).
People may join in to battle against the player with someone else on certain routes.
New cut scenes involving Groudon, Kyogre, and Rayquaza can be seen during certain parts of the game.
Pokémon have animations before battle, as in Pokémon Crystal.
The story involves both Team Magma and Team Aqua, and new events involving them occur.
The gyms' layouts have changed, and the Pokémon of the Gym Leaders and members of the Elite Four have changed (this excludes Phoebe's and Glacia's teams).
Wallace, the Gym Leader of Sootopolis City in Ruby and Sapphire, has been replaced by Ardan, who is also a water trainer. Most of Wallace's team has been altered.
For whoever knows what happened to Steven: he is now in Meteor Falls. He has no alterations to his team.
The player can battle the Gym Leaders again, with the Gym Leaders having improved Pokémon teams.
Some Gold/Silver/Crystal Pokémon not available in Ruby/Sapphire are now catchable after the Elite Four is defeated.
A new park called the Battle Frontier, which replaces Battle Tower's island, has seven different zones with varying rules.
A new exclusive Deoxys form can be obtained: Speed
The game comes packaged with the Wireless Adapter and is compatible with FireRed and LeafGreen in this respect.
One can obtain the same tickets from FireRed and LeafGreen for acquiring Deoxys, Ho-oh, and Lugia. In addition, a new ticket is used for acquiring Mew at a place called World's Edge Island. As usual, the tickets are only obtainable at a Nintendo event.