I think you could have a minimig that utilises both an FPGA with integrated PowerPC core (some Spartans have two!), and another FPGA for the "AGA++" type chipset. A 68k could be programmed onto the former FPGA for backwards compatibility. You'd run a fast bus between the two FPGAs.
Hopefully that would be able to run AmigaOS4 on the PowerPC part, whilst still having native capabilities of the classic Amiga.
Of course it should be done one step at a time, and if you want an uber-amiga then I don't think that any evolution of minimig will be the best way to achieve it.