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Pokemon's Creation & Game Freak - Did You Know Gaming? Feat. Tamashii Hiroka
Pokemon & Religion - Did You Know Gaming? Feat. Jimmy Whetzel
 
The order that your rival Brenden or May sends out their Pokémon during battle is determined by which gender they are and, thus forth, is also determined by which gender the player chose for their own character before their adventure started. However, for reasons unknown, this only works if the starter the rival choose was Treecko.
Contributed by PirateGoofy
The player can completely softlock their game if an extremely complex and absurd series of actions are undertaken, forcing them to have no other choice but to start a new game. Specifically, if this is done, then the player will be stuck at either the Pokémon League building, Pacifidlog Town, Dewford Town, or Sootopolis City with only an Electrode that only knows the move Selfdestruct.

This is not possible in the Generation VI remakes.
Contributed by PirateGoofy
The Mirage Tower, exclusive to Emerald, may be a reference to a tower with the same name which appears in Final Fantasy. Both appear in a desert, only appear under certain circumstances, and contain a spiral-shaped dungeon.
Contributed by CuriousUserX90