You can see a list of changes at the Crystal Clear github; it's a massive update. New features include:

• A revamped Pokedex that shows a Pokemon's base stats, more detailed info on its locations (specifically the levels it can be found, how it can be found, and encounter rate), and evolution methods.
• You can start in any town or city in Johto and Kanto and you now get your own residence that you can customize.
• Pokemon can be tracked down in the wild from their footprints using a new item.
• Alternate palettes for Pokemon based on nicknames.
• New maps, including the Underground Arena (located at the Kanto Underground) and Goldenrod Cafe.
• More quality of life features, such as a message that appears if you encounter a shiny Pokemon in the wild.