Treating this purely as a 'fantasy' Amiga games console that has no chance of ever happening...
I'd go with:
CPU: 2Ghz PPC
BUS: 32-bit custom architecture (nothing really to be gained from being 64-bit)
GFX: 32-bit custom 3D graphics chip (if it were to use an existing solution like ATI or NVidia, then there would be nothing 'special' about it, people would just stick to their PC's)
RAM: 1GB RAM
OS: None, it's a games console!
Ports: USB 2.0
CDROM: DVD 16x
CASE: Sleek, compact, brushed-aluminium.
...and a name like 'Amiga CD64' is too geeky in this day and age. Something like the 'Amiga Vision' or 'Amiga Future' games console would sound much better, especially from a marketing point of view!
Steve.