I think the possibility of an FPGA-based Amiga will make more sense than the X1000's Xena chip. That way it will run most Amiga software without need of an emulator. Even with the raw horsepower that PA-Semi's PPC chip offers, the X1000 will be hard-pressed to emulate some games at full-speed.
The only other option besides an FPGA would be to translate most of the functionality of the Amiga AGA chipset into shaders and run them on the graphics card. In the end I suspect both solutions will be adequately explored.