Had my A600GS for a few days now, after I got some initial issues out of the way I'm having a great time with it.
This and "TheC64" (my other great purchase a few years ago) sure beat emulation on a boring old PC.
- Ability to choose smaller icons or perhaps a list view in the games selector.
- Ability to map keyboard keys to joystick (as per UAE, cursor keys + ctrl)
- Ability to map a joystick button to Up (and disable Up on the joypad)
- Disk drive noise 
These.
Re disk drive noise: some people may not like it, but it would be nice to have it as a selectable option for those that do/those that want it there as a reassurance their A600GS has not crashed on long load times that some games have.
Joystick mapping needs to be done, particularly for racing games where you have to push up all the time to accelerate, that's murder on my thumb when I do it using the d-pad. So an option to map joystick movements and also keyboard keys to buttons on the gamepad.
Option for smaller icons/list view (list preffered) for the launcher to minimise amount of scrolling when I ultimately get a ton of games installed, and AmigaBill's suggestion of folders in the launcher would be great too!
Also a web browser to run inside AmiBench as some others have suggested.
(edit: fixed typos)