I still think it's fully possible to build an AT/ATX A1200 compatable board...
Start with a 68060 cpu. Decode the logic from the original chipset and write it to PLDs. Leave out unnecessary parts (such as the original AGA video, sound and PCMCIA). Add PCI support, and use RTG exclusively. Change out the CIA chips for modern UARTs. Use the Catweasel chip as a floppy controller, so you can use a regular PC floppy drive and still use Amiga floppies. Stuff like that...
Hell, most of the work has been done already by Elbox, IC, and others.
Someday I hope to build this board myself. :-D