For the face buttons, perhaps a six button layout ala the Megadrive/Genesis? If it didn't make the controller too large it could mean extra buttons when combined with four on the shoulders. Brilliant for fighting games.
Also this is a great idea for 3D printing.
Six face buttons is definitely something I'm considering, I'm just having a hard time reconciling that with the diamond shaped layout that most other games expect by default.
Mad Catz FightPads sort of address this by making both rows arc-shaped, which might be an option here.