Personally I'd like to be able to use keys as mouse buttons. One of the ways I fight hand and finger fatigue on windows is to map F2 to the left mouse button and use a trackball. On the windows side I used autohotkey for this; I haven't been able to find a good equivalent under linux that allows key-mousebuton mapping.
Why not take it further and allow game controllers and other inputs to control standard mouse and keyboard functions?
Getting my own keyboard layout to work has been so far biggest obstacle to use linux at all. GUI for easy custom keyboard layout creator embedded to keyboard settings is in top of my wishlist. I might be wrong but is it not possible to add any unicode character to layout with XKB, for example μ (mu) for easy typing of abbreviation of micrometer? I belive here ability would certainly create usage.
In windows one can change typing layout but keep shortcuts as they were. This would also be most useful but might been harder to do.
This needs to be done, in my opinion. I managed to create my own custom keyboard layout, but it was scary. And broke things a couple times. Even now, sometimes the keyboard layout will revert to the default of the category rather than my custom layout (which is a modified version of the default of the category).
Also, being able to map usb devices + mice to key presses would be awesome. There is a project that's trying to do this (joy2key). But I haven't been able to get it working. And JoytoKey, the Windows equivalent, will only work within the Wine window within which it's running, making it pointless.
If the point of Linux is the amazing ability to customize, this is absolutely necessary to keep that image.
But yes, it should definitely be an "advanced option"
This is an excellent idea, as I think that you should be able to remap your keys without needing to use xmodmap. For some people, like myself, remapping is vital. My + and 'L' keys were ripped out by our cat as it walked across the table, and every time I turn on my computer I have to go to the terminal and reconfigure my setup.
This would be an excellent implementation into the Keyboard preferences.