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* It is now possible to Fly to the [[Pokémon League Reception Gate]]. It is also now possible to Fly between Indigo Plateau or the Reception Gate and any location in either Kanto or Johto. Curiously, however, it's not possible to Fly to the [[Pokémon Center]]s in [[Route]]s {{rtn|4|Kanto}} and {{rtn|10|Kanto}}, whereas it was possible in FireRed and LeafGreen, but not in the original Gold and Silver.
* The clock reset interface from the original Pokémon Gold and Silver was removed, as was the case with {{game|Crystal}}. In its replacement is a microphone test interface that can be accessed via the button combination X, Y and Down on the title screen; though this feature, unlike the clock reset interface has been officially mentioned by Nintendo via the game instruction booklet.
* Any special Pokémon, such as {{p|Sudowoodo}}, will respawn to their specific location after the player defeatsenters the [[EliteHall Fourof Fame]] if they were defeated instead of caught the first time.
* The ability to decorate the player's room, a feature introduced in the original Gold and Silver, is absent.
* After defeatingentering the EliteHall Fourof Fame, [[Professor Oak's Pokémon Talk]] can identify [[mass outbreak]]s daily when accessed through the [[Pokégear]]'s radio. This also includes the six Generation II Pokémon whose outbreak formerly occurred when a specific trainer whose number that was stored in the Pokégear would contact the player to report the outbreak during Generation II.
* Physical and special moves are now determined by the move itself rather than type.
* The Regional Pokémon which previously had to be transferred from [[Generation I]] are now available [[List of in-game event Pokémon in Generation IV|in game]].
As in {{game|Gold and Silver|s}}, the primary Pokémon of the remakes are native to the Johto and Kanto regions. Due to advances in gameplay since the second generation, the regional Pokédex used in Gold and Silver (the [[List of Pokémon by New Pokédex number|New Pokédex]]) has been updated to include those Pokémon which [[evolution|evolve]] upon learning a new [[move]]. Rather than simply excluding these evolutions (as {{game|FireRed and LeafGreen|s}} did with [[friendship]]-based evolutions), an improved [[List of Pokémon by Johto Pokédex number|Johto Pokédex]] was established with 256 Pokémon: five more than the New Pokédex.
Similarly to other recently released Pokémon games, Pokémon from outside the regional Pokédex can be captured after defeatingentering the [[EliteHall Fourof Fame]] and earning the [[List of Pokémon by National Pokédex number|National Pokédex]]. Pokémon native to Sinnoh and Hoenn can be found in various methods. [[Mass outbreak]]s of Pokémon sometimes break out across the Johto and Kanto regions; oftentimes these are not native to either of the regions. Pokémon from other regions can be located by playing one of two special stations on the [[Pokégear]]'s radio function. There is a channel for Sinnoh Pokémon which plays only on Thursdays; the Hoenn channel only plays on Wednesdays. By having either of these programs turned on when in [[tall grass]] the chance of finding a foreign Pokémon increases. The [[Bug-Catching Contest]] also hosts, from time to time, Hoenn and Sinnoh Pokémon. They will only appear on Thursdays and Saturdays. The [[Johto Safari Zone]]'s customization option also allows for the finding of Pokémon from other regions. Trainers in Kanto (which is accessible after obtaining the National Pokédex) often have Pokémon from Hoenn and Sinnoh. All [[Gym Leader]]s except [[Clair]] use at least one Pokémon from Hoenn or Sinnoh in [[rematch]]es.
In an apparent attempt to remove reliance on [[Generation III]] cartridges, [[starter Pokémon]] of Kanto and Hoenn can be obtained late in the game from [[Professor Oak]] and [[Steven Stone]] respectively. Some [[legendary Pokémon]] which were not included in the [[Generation II]] games, such as Kanto's [[legendary birds]] and {{p|Mewtwo}}, are also available.