Being able to upload eeprom via eemem keyword would be neat, but we could actually do this a sneaky way, without adding any extra code to the bootloader: the upload utility on the computer could scan the .hex file for eeprom segments, and if it finds any it could instead package them in to an eeprom upload program, write that, run it, then automatically boot back in to the bootloader and upload the user's program. This way you could have the extra functionality without having to store the eeprom writing code and extra usb interface stuff in the bootloader on the chip permanently - reducing how much space is available for programs.
That's really the core of the issue - adding eeprom support right in to the bootloader doesn't really make sense from a space saving perspective because it would make the bootloader fatter, so you would be trading flash for programmable eeprom, but most people wouldn't even use the eeprom anyway, and it's still fairly straight forward to write a program which sets stuff in eeprom to do your initial setup.
As for eeprom as a communications medium, I've thought a bit about that too but it seems not so useful, since it only works for a few seconds after you plug the device in to the USB port.
Still, it's an interesting idea. Maybe it'd be smarter to add a flash read function - then it could fully verify uploads, and if you need to do eeprom stuff only, it could download the current one, upload eeprom utilities program, run it, and when done automatically load back in the program from before then.