I *REALLY* like your idea of custom button configurations for some games, but we need a generic layout too for the rest of the games. i kinda see you mapped C-buttons into top right screen (ocarina) but can't see anything more, maybe because of transparencies. Did you check this? i like the grey ones.

And about the GUI, well is there any way to tweak the emu ingame? without typing variables in command line at start up, like tweak the frameskip without close the game?