Although they aren't 100% hardcoded into the game, the textures for the sky and certain colors can be tricky to modify because you need MCPatcher/Optifine in order for them to work in the first place, which is assuming you know exactly what files to add and what to edit (and in some cases like the swamp color, you can't change them at all). It would be nice if these files were readily available and easier to change, like other resource pack files, without needing to download mods. Maybe in 1.13-14?