I don't like having to constantly copy and paste my shaderpacks from instance to instance, I figured it would be nice to have a config option or ingame setting to include "%appdata%.minecraft\shaderpacks" in the shaderpack list.

One way to avoid copy pasting files between multiple locations is using symbolic links. On windows something like mklink /D instance_path\shaderpacks %appdata%\.minecraft\shaderpacks would work, and has the benefit of being able to be used for more than just shaderpacks (i.e. shared resource packs, configs, saves).

That's definitely a great and elegant solution to the problem (I didn't even know it existed), thanks for the answer! Though I still think it would be a nice qol thing to have ;p