From Bulbapedia, the community-driven Pokémon encyclopedia.
| Various images from the pre-release, courtesy of Game Freak
Pokémon Crystal introduced many features that have since become staples of the main series games, such as the option to pick a female player character, animated Pokémon sprites and battle facilities with special rules. Likewise, some aspects of the game's initial design did not make it to the final release. However, the game has very few beta elements compared to its companion games, Pokémon Gold and Silver, likely because it is heavily based upon these games.
Although Kris was introduced in Crystal, a development picture reveals that another girl was in the works. The girl had black hair in pigtails. She may have also been an attempt to include the unknown female Trainer that was seen in artwork released during the development of Gold and Silver.
Pokémon Communication Center
A development picture revealed an early design of the Pokémon Communication Center. Fundamentally, the differences from the final design include an upper floor on the top-left of the map and two machine areas in the main floor instead of just one, one of which was replaced with a Trade Corner for use with the Pokémon Mobile System GB in the final release.
Super Game Boy features
Despite Pokémon Crystal being incompatible with the original Game Boy, Game Boy Pocket, Game Boy Light, the Super Game Boy and the Super Game Boy 2, there is an unused Super Game Boy border programmed into the game, which can be activated by setting a flag in the game's code to enable the Super Game Boy features. Cheating devices such as the Game Genie can also be used to achieve the same effect, albeit only temporarily. The border is a leftover from the Japanese version of Pokémon Gold, since the design is the same and the text reads "POCKET MONSTERS GOLD VERSION", rather than "POKéMON GOLD VERSION" as it does in the English version of Pokémon Gold. This could also suggest that Game Freak used Pokémon Gold as the basis for the development of Pokémon Crystal.
If the player attempts to play the game on a model of the Game Boy prior to the Game Boy Color, they will receive a screen with a message saying "This Game Pak is designed only for use on the Game Boy Color." with the word Crystal spelled out with Unown. There is an unused color palette associated with this message, using an orange tint, with text saying, "Pocket Monsters Gold Version".