I'm working on this, those days.
Amazing work.
Since Arduino insists on having a serial line to upload the firmware (although none is needed for usbasp), you may have to edit Arduino's preferences.txt file manually and set the variable serial.port to an existing device. Preferences.txt is in ~/Library/Arduino on the Mac.
With Arduino 11 the serial pb will disappear (not tested yet but something like metaboard.upload.disable_flushing=true will solve the pb)
If you are running Linux like me you will have to set udev rule in order to allow the avrdude process to upload sketch (see http://forums.obdev.at/viewtopic.php?p=4436)
I think a timeout bootloader will be better than the jumper selectable boot mode.
Perhaps it will be better to rewrite completly the bootloader in order to have a CDC metaboard (but perhaps it will load to much the CPU).
This way you will be able to use serial.prints/reads to talk to the host
I'm sure il will be possible to make a simple arduino (able to program other avr, do a serial to usb converter, etc) at a very very low cost (10$ removing the external power regulator)
Nicolas