A female player character, Kris, was introduced, marking the first time players could choose the gender of their character. The choice is purely aesthetic and does not affect gameplay or story.
When entering a new area, its name appears on-screen for a brief time. This would become standard for the rest of the series.
The Ice Path was redesigned with an ice-like appearance. Some of its puzzles were also changed.
The Burned Tower was redesigned on the exterior and interior. The outside was altered to look more liked a burned building rather than a short one (see the Burned Tower page for more information).
Lance's room at the Indigo Plateau was redesigned to have a draconic appearance, with the statues in the room being replaced with Dratini statues.
Raikou, Entei, and Suicune have their own special battle music when the player encounters them in the wild, making Crystal the first game to sport special Legendary Pokémon battle music.
The Dragon's Den was subtly altered; now the Dragon Shrine is open, and some Headbutt trees were added to the back of the Shrine.
The Goldenrod Department Store had a roof area added.
More work was done on Pokémon sprites:
Pokémon sprites now play a short animation upon entering the fight and a longer one when the Pokémon's profile is viewed, a feature that would not be seen again until Pokémon Emerald. In this game, only the front sprites are animated.
While most of the Pokémon retain their sprites from either Gold or Silver, certain Pokémon, such as Houndoom and Croconaw, were given new ones. This includes some Pokémon who had identical sprites in both original versions, like Sneasel and Suicune. The W Unown was redesigned, its new design was used in all future games.
A few Pokémon, such as Spinarak, Magnemite and Sneasel, were recolored to more closely match their official artwork.
Several of the Pokémon that were redrawn gained new back sprites.
The user interface used during Game Link Cable trades was redesigned. Gold and Silver used a simple black on white trading interface that was identical to the one used in the Generation I games, mainly to retain compatibility with older Game Boy systems. In Crystal, the menus were revamped with full color on a black background, a design which better suits the capabilities of the Game Boy Color.
A fountain was added to the center of the pond in the National Park.
The inside of Mt. Mortar was changed.
Certain Trainers have their dialogue changed.
Extra grass was added to Route 36, west of Violet City, and in this grass, Growlithe can be caught, allowing players to acquire a Fire-type Pokémon much earlier than in other versions (assuming they did not choose Cyndaquil), and making a large difference in the availability of Fire-types for areas like the Azalea Gym and the Sprout Tower, where Fire-types are super effective.
Just like in the Japanese Pokémon Blue and all releases of Pokémon Yellow, changes were made to available wild Pokémon:
On one hand, several Pokémon that were exclusive to Gold or Silver are available in the wild, like Gligar and Skarmory. On the other hand, some species that were available in both Gold and Silver are a no-show this time around, like the Mareep family.
Sneasel appears in the Ice Path, whereas in Gold and Silver, it did not appear until reaching Mt. Silver.
Magmar no longer appears in the Burned Tower, instead appearing exclusively in Mt. Silver.
Some of the wild Pokémon that appear in Kanto were altered.
Some Trainers were repositioned on the map.
Several new Trainers were added, some of which could only be battled when certain conditions are met. For example, Pokéfan Jaime on Route 39 can only be battled at night. Some of them won't approach the player themselves, and, when spoken to, won't play the "encounter" music before engaging in battle.
A Battle Tower, the first in the series, was added to the north of Route 40.
Ho-Oh cannot be caught until Raikou, Entei, and Suicune are all caught.
Changes were made to the Ruins of Alph. This included more common Unown, as well as a new subplot—completing enough puzzles allows the player to read a secret message left behind by the Unown. It suggests that the Unown were left behind by the ancient civilization that constructed the Ruins of Alph, and that the statues that line the interior were made by those people.
Previously, Trainers who called on the cell phone all said the same phrase, with only the names of the Pokémon they reference changing. Trainers are now given distinct personalities (one talks about shopping, another about grooming), and call for reasons other than battling, such as giving the player items, or informing them of a rare Pokémon appearing (Wade gives the player Berries, Alan gives them a Fire Stone, etc.).
The Buena's Password radio show was added, which players can listen to on their Pokégear and receive points in order to redeem prizes.
The new rooftop area of the Goldenrod Department Store has occasional sales, which the player is informed about if Camper Todd's number is registered in the Pokégear.
The function to reset the clock in non-Japanese and non-Korean versions of Gold and Silver remains, although it is now more difficult to access.
On the title screen, the player must first hold the ↓, SELECT, and B buttons.
While holding SELECT, they must release ↓ and B.
Still holding SELECT, they must now hold ← and ↑.
Finally, the player must release SELECT.
Kurt can now make multiple Balls from same colored Apricorns simultaneously.
The Odd Egg was added to the game.
Some Pokémon have changed level-up movesets, however, all but one of them have only one change.
Some bugs with the battle mechanics were fixed; however, the game performs a check when it detects a Link battle to use the older and buggy mechanics in order to maintain compatibility with Pokémon Gold and Silver. This occurs even between linked players of Pokémon Crystal games.
Likewise, the game also performs a check that partially converts Kris into Ethan at the Cable Club and Time Capsule rooms, even if all the players using the Cable Club rooms are specifically playing Pokémon Crystal.
Suicune, instead of being a side Legendary Pokémon, has a prominent role in the game's storyline. Awakening the Legendary Beasts is now a prerequisite for challenging Morty. After this, the player will constantly find Suicune in various locations throughout Johto. After receiving a Clear Bell (where in Gold and Silver, the Rainbow or Silver Wing would be obtained instead), the player will have a chance to battle and capture it in the Tin Tower, and it will not run away.
A new character, Eusine, is added to the game. He is searching for Suicune as well, and will battle the player in Cianwood City to earn its respect.
The chain of events to obtain the Rising Badge is altered. Where previously, it involved a trip to the Dragon's Den to retrieve the Dragon Fang, it now involves entering the Dragon Shrine within the Den. There, Clair's grandfather and leader of the dragon-user clan quizzes the player on their style of battling. Clair arrives and still refuses to hand over her Badge after the player passes. In response, her grandfather threatens to tell her cousin, Lance, of whom Clair is terrified. If all the questions are answered correctly, the player will receive a Dratini that knows ExtremeSpeed upon returning and speaking with Clair's grandfather.
Vulpix, Mankey, Mareep, Girafarig, Remoraid, and their evolutions can't be obtained in Crystal.
Also, if you get Crystal on Virtual Console, then Celebi is supposed to be obtainable.