Pokémon Colosseum beta
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Early title screen cover art logo
The bonus disc cover art for the US version of Pokémon Colosseum shows an earlier version of the English title screen logo that retains the Japanese release's brick background.
Various screenshots found on different gaming websites and some gaming magazines show different designs for various parts of the game. The most notable change showing a very different version of the HUD display.
Unused Shadow Pokémon e-mails
The game contains some e-mails that are never sent to the player character showing an encounter with a Shadow Kecleon at various locations and more Shadow Pokémon were meant to occur at some point in development before being scrapped. Minun, Spoink, Castform, Psyduck, Porygon2, Whiscash, Wobbuffet, Wailmer, Xatu, Baltoy and Kecleon are never obtainable in the final game. In addition, while Plusle is given as a gift to Wes; Minun cannot be obtained anywhere.
Magcargo's pre-evolution, Slugma, and Teddiursa's evolution, Ursaring, are available in the final game. Baltoy, Xatu's pre-evolution Natu, and Psyduck's evolution Golduck, would later become available as a Shadow Pokémon in Pokémon XD: Gale of Darkness.
I obtained the hard-to-find SHADOW KECLEON! It's a trivial thing. Only the person who knows the password of this mail's title will battle. They're waiting just before Pyrite Colosseum!
I obtained the hard-to-find SHADOW KECLEON! It's a trivial thing. Only the person who knows the password of this mail's title will battle. They're waiting at the entrance to the Shadow Pokemon Research Lab!
I obtained the hard-to-find SHADOW KECLEON! It's a trivial thing. Only the person who knows the password of this mail's title will battle. They're waiting at the entrance to Team Snag'em's hideout!
Hi, it's NETT. I analyzed the SHADOW POKéMON LIST again and discovered six more. The additions are SKIPLOOM, QUAGSIRE, SUNFLORA, FURRET, MAGCARGO, AND MINUN. I'll send another update if I can find any more.
Hi, it's NETT. I analyzed the SHADOW POKéMON LIST again and discovered six more. The additions are ARIADOS, LEDIAN, SHUCKLE, MISDREAVUS, SPOINK, and ABSOL. I'll send another update if I can find any more.
Hi, it's NETT. I analyzed the SHADOW POKéMON LIST again and discovered six more. The additions are HITMONTOP, REMORAID, MANTINE, MEDITITE, BALTOY, and KECLEON. I'll send another update if I can find any more.
Hi, it's NETT. I analyzed the SHADOW POKéMON LIST again and discovered six more. The additions are SWABLU, CASTFORM, SMEARGLE, GLIGAR, STANTLER, and MURKROW. I'll send another update if I can find any more.
Hi, it's NETT. I analyzed the SHADOW POKéMON LIST again and discovered six more. The additions are PILOSWINE, FORRETRESS, GLIGAR, SNEASEL, PSYDUCK, and TEDDIURSA. I'll send another update if I can find any more.
Hi, it's NETT. I analyzed the SHADOW POKéMON LIST again and discovered six more. The additions are HERACROSS, PORYGON2, WHISCASH, XATU, WOBBUFFET, and WAILMER. I'll send another update if I can find any more.
There is one line of dialog cut from the game in the game's internal data. It was most likely a reference to a battle with a trainer called SHADOW GRASS POKéMON KING who beyond having their trainer class name in the game does not have any other data attached to them.
Eh!? Chimecho isn't a Grass Pokémon... It's a Psychic Pokémon.
There are some trainer classes that are never used. As they only have names and nothing else, it is most likely they were scrapped very early in development.
HUNTER RETAY - Unused Hunter trainer
MALPES THE RIDDLE-LOVER
SHADOW GRASS POKéMON KING
Six Shadow Aipom Siblings - May have been an early version of the Hexagon Brothers that are encountered in the game's sequel, Pokémon XD: Gale of Darkness.
There are several unused Level 100 Pokémon teams with blank movesets that would have been used by a Snagem Head Class that also go completely unused.
Rui also interestingly has a Trainer graphic and model for standing behind Pokémon in battles, she might have been battled at one point in time. 
An Ability known as Cacophony was found within the internal data. No Pokémon has it legitimately; a Pokémon can only have this Ability by modifying its data. It is identical to Soundproof, another sound-based Ability, and it allows the Pokémon to avoid all sound-based moves. Since it is identical to Soundproof, it was likely scrapped due to redundancy, and some Pokémon that have Soundproof may have originally been intended to have Cacophony instead, such as Loudred and Exploud, which are well known for their loudness.
Unobtainable Shiny Celebi
For the sake of consistency and to prevent game crashes if they are hacked into the game, every Pokémon has a Shiny variant. However, as Celebi was distributed only through the Japanese Pokémon Colosseum bonus disc and locked to never be Shiny, it is impossible to legitimately obtain a Shiny Celebi.
While the e-Reader content was removed in the international localizations of Pokémon Colosseum, the theme used for the e-Reader menu screens is still in the game's internal files.
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The e-Reader room is present within international versions of the game but has been made impossible to enter without cheating. Translations had made significant progress before being scrapped, likely due to the poor sales of the e-Reader device outside of Japan. The letter in e-Reader uses a different font style not used anywhere else in the game or game data. In the European release of the game, all dialog present in the room is blank and interacting with anything will bring up empty text boxes.
US bonus disc game compatibility
The internal data for the US bonus disc shows compatibility for Pokémon FireRed and LeafGreen have been disabled by default. Compatibility with those games is impossible without modifying the ID values on the US bonus disc. There is no compatibility for Pokémon Emerald as the game came out much later.
Japanese bonus disc translations
The content from the Japanese bonus disc was mostly left in the game but the translation for it was never completed and some items are mistranslated. The Light Ball that Pikachu holds is mistranslated as LIGHTBULB. Additionally, data for the Ageto Celebi is present on the main game disc despite only being available from the Japanese bonus disc.
Relic Stone map file
The Relic Stone map within Agate Village is listed as shrine_1F internally even though there is no floors leading to the Relic Stone. There may have been more maps planned at some point between Agate Village and the Relic Stone.
Unused e-Reader content
The e-Reader content is in the English localization of Pokémon Colosseum and also includes data for an unused and unreleased 21st Pokémon e-Reader card.
In the international localizations, Rui's skirt and shirt were made longer.
Unobtainable Shadow Pokémon encounters
Due to the e-Reader room being dummied out in the international releases, three more Shadow Pokémon are not normally obtainable. Encounters with the Trainers that would have had Mareep, Togepi, and Scizor are not possible in the international releases without hacking the game.
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