Hi,
As the Gameboy shader was impacting the in-game performance too much, I used lib-gambatte custom palettes.
I specified this in a comment on Reddit:
https://beta.reddit.com/r/RetroPie/comments/3m1uje/how_can_i_play_gameboy_games_in_the_original_green/cxixgyx
Using the dot.glsl shader in addition to this allows a nice GB image while maintaining good performance.