I'd like the shell to be like a Wavebird in shape, but the button layout should be different. It should be a SNES diamond-style layout BUT on the top right of the diamond there should be another button. Like this..
Then, there would be a Z button at the top like the Wavebird, except it would be made a lot better (easier to push, more comfortable to rest finger on etc)
So to play NES games, you can use the NRC or the shell (left buttons). To play SNES games, you would use the normal diamond layout and the shoulder buttons of the shell.
To play N64 games, you have A&B as the left buttons, then on the right you have three others. These would be C-left, right and down. C-up would be the Z button.
GameCube games can also be played.
Finally, I would replace the C-Stick with an analogue stick and upgrade the D-Pad.