I have been thinking about something like this... maybe using the Propeller chip as controller. The trick would be connecting to the Amiga. Do the ARM chips have the old school address & data bus interface to memory, or just SPI? I suppose you could use a sort of clockport style interface and have a service routine on the ARM do the grunt work of reading it then passing it off to or from the I/O devices.
That's what I was thinking. The reason that is always given on why these retro systems cannot use USB is because the system (real retro) or the system they are recreating cannot handle the USB load, and don't have the USB software stack to handle it.
By doing all of the USB on the Arm, and just outputting in whatever format is the most convenient for the retro system, the ability of the retro system to handle a USB stack becomes irrelevant. At the very least, it should be trivial to make a USB gamepad/USB keyboard/USB mouse to 9-pin joystick/PS/2 keyboard/PS/2 mouse adapter. This would give all of the new retro systems the ability to use new periphrials.
Making data storage and network would be a little tougher, but shouldn't be over the top hard.