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I've made a small patch that changes most of the color palettes of shiny Pokémon in Emerald. The intent behind this project was to make every shiny Pokémon feel special, and not just plain ugly (most green shinies are gone for this reason). There's no repointing in this patch, so it'll map to...
If you're compiling the Emerald Battle Engine Upgrade from the master, make this change. Worked for me, but I haven't bug tested it thoroughly yet:
In the file "battlescripts_for_moves.s", on line 1772, remove "| 0x80" from the end of the line. So it should go from reading this way to this way...