Special Pokemon

Shiny Pokémon
A shiny Pokémon is a specific Pokémon with different coloration than what is usual for its species. These mutations often have slightly better IVs (individual values) than other non-shiny Pokémon, but the difference is nearly negligible. As is normal in Pokémon games, you have a 1/8192 chance to get a shiny Pokémon. However, there are special opportunities in Zeta/Omicron during which you can obtain specific shiny Pokémon. A few Pokémon have gotten new alternate sprites for Zeta/Omicron as the official ones are very similar to their normal coloration.
 * In the Blackfist Department Store, you can purchase the Rare Egg, which then hatches into a shiny Gible.
 * A shiny Steelix can be obtained from the Andromeda Mines.
 * An unlimited number of shiny Unown can be obtained in Wonder Cave after obtaining Rock Climb and Rock Smash.
 * Completing the Solo Challenge will award a Shiny Jirachi in Zeta or a Shiny Victini in Omicron.

Shadow Pokémon
Found in the Aroma region, they are the only Pokémon you can catch from other trainers. * Miror B's Pokémon levels will match your own. If you have not caught every single Shadow Pokémon up to that point, his Shadow Pokémon may instead be something from the pool that you failed to catch.

**These Pokémon are not needed to obtain the reward for acquiring all of the Shadow Pokémon.

Clone Pokémon
Used by Mewtwo in your battle against him on the Police Mission 6. Appear to be the same as normal Pokémon, and cannot be captured unless through means of third party programs.

Fakemon
Fakemon are mostly used by non-playable characters and are thus unobtainable by the player in-game. There are a few exceptions, however.

Ausitto can be evolved from starting from level 50. It is capable of learning every ten levels.

Obtainable Delta Pokémon
Can be encountered in some places by using Rock Climb or in the Delta Temple (use Tesseract on the grass part on the beach in Yangtze Town).

Unobtainable Delta Pokémon

 * Delta Ninetales - Used by Delta Leader Neal at the Delta Temple
 * Delta Raichu - Used by Delta Leader Talde.
 * Delta Blastoise - Used by Delta Leader Talde.
 * Delta Charizard - Used by Delta Leader Talde.
 * Delta Aerodactyl - Used by Delta Leader Talde.