There's an unused sprite in Pokémon Ruby and Sapphire that appears to be a revamped (and stretched) sprite from Game Freak's first game, Mendel Palace.

There are 2 unused abilities. No Ability and Cacophony.
No Ability is presumed to be an error handler, and is used when the game manages to find a Pokémon with an ability of ID set to 00. The term isn't used in the final game because all Pokémon were given abilities.
Cacophony is an ability similar to Soundproof, which isn't assigned any Pokémon in the game. It's assumed it was meant to be the ability for Whismur, Loudred, and Exploud, given their nature for noise-based attacks.

An unused sprite for a member of Team Aqua exists in the internal data and is identical to that of male Team Aqua Grunts with the exception of a mirrored body, modified coloration, the addition of a mustache, and a bandanna around the Grunt's left arm.

Two of the optional male names at the start of the game (one in Ruby and one in Sapphire) refer to "land" and "sea" respectively. In the English version, these are Landon and Sean; in the Japanese version, リクヤ Rikuya and カイト Kaito (陸 riku means land and 海 kai means sea). This is also the case in other languages.

When playing as a female, two other optional names are also available: Terra and Marina.

Junichi Masuda stated that while developing Pokémon Ruby and Sapphire, Game Freak considered changing the number of Pokémon the player can have in their party, and the number of moves a Pokémon could learn. The idea was later scrapped. It is currently unknown what sort of potential changes were to be made.

Ruby and Sapphire were the first Pokemon games to introduce Abilities. These introduced new strategies for Pokemon battles. Some examples include Levitate, which makes the Pokemon immune to Ground moves, and Vital Spirit, which prevents sleep.

In Pokémon Ruby and Sapphire, map data exists for a closed version of the Flower Shop (which in the final version is usually always open) on Route 104. In this unused map there is only one non-playable character, and they inform the player that the Flower Shop is closed.

The map was originally used in the Pokémon Festa 2002 demo to limit the player's experience of the game. It was later removed from gameplay in the final version, but still exists within the code.

Many sprites of the backs of Pokemon are actually minor edits of sprites from Gold, Silver and Crystal, with Farfetch'd, Caterpie, Weedle and Kakuna being almost identical to the previous sprites, simply having an extra shade or two of color and updated palettes.

There is an unused battle theme for the three legendary beasts, suggesting they were planned to make a return after Gold, Silver and Crystal. The legendary beasts made a return in FireRed and LeafGreen, and could have been an implementation of the original idea to put them into Ruby and Sapphire. It's also possible the track was simply used for testing purposes.

The Team Aqua/Magma Leader Battle theme music featured in Pokémon Ruby, Sapphire and Emerald is based on the Shionchou boss battle theme music from Game Freak's Super Famicom game Bushi Seiryūden: Futari no Yūsha. The themes were written by both games' composer and Game Freak co-founder Junichi Masuda.