My requests (trying to not repeat what others have requested):
- Software mouse cursor that is placed at the depth of what it's pointing. I use 3D Vision and it would help immensely whenever I want to click on an element.
- Overclocking feature, like FCEUmm has. There are games that have slowdowns in the real console and this would fix it.
- Configurable number of layers, maybe.
- Save states, speedup, rewind, etc (typical emulator features).