I would have thought the minimig AGA would have been ideally suited since it's both mini-itx and about as close to a "propper" Amiga as one could hope to get.
You could fit 6 of those in a A2000 case.
I kind of like the idea of putting a windoze UAE machine in an A2000. Go for it I say. You should be able to match up the slots (STD ISA spacing)
Could be quite a beast....