IMO USB isn't suitable for Minimig, but lets consider it:
To be of any use the USB-stack would need to run outside of the emulation in the first place (this is kind of obvious if you think about it: How would you go on about launching the USB-stack if you're booting from a game floppy? You obviously want to be able to use the keyboard and mouse in games...)
IMO the only sensible way would be to have some sort of independent USB-on-chip solution that'd give PS2-like signals easily, without actual need to have custom USB-stack. That'd be "easy" (relatively speaking) to wire to the current Minimig design.
However, once the USB is outside of the emulation itself, it means that the running system will not get any real benefits from the USB in the first place (actually, it won't see USB at all, just keyboard and mouse/joystick thru the CIA/Custom registers).
In fact, you'd get much of the same (except amiga joystick) by connecting some external USB-to-PS2 bridge to current minimig.