Well, if he already had a C=One board, I can see why he would start there.
Clearly now that the C=One board is clearly not enough to do a full Amiga of any sort he needs to consider his options, and I hope he takes a long hard look at the MiniMig as a potential platform to port to.
Of course, for AGA he'd need for video outputs - 24 bits instead of 12 bit. Also the CPU is probably a weakness for his design. Taking it to the extreme a different motherboard with a soft-68k and AGA+ is the most flexible option, but also the most expensive. Using a discrete 68k is also a very expensive option.