One advantage of the FPGA is that you can reprogram it to do something else after you're bored with it acting as a C64, assuming in this case that you are able to desolder it. Also might only make sense to reuse the FPGA if it is sufficiently expensive. Another advantage of using an FPGA is that if you make a mistake in your design you can easily correct the error at any stage and resynthesize it.
There have been other retro computers built, and one of the features that's pretty common is the ability to emulate multiple systems. The Turbo Chameleon 64 (which can act as a C64 itself or can be plugged into a real C64 to accelerate and expand its capabilities) can also run an Atari 2600 image, as well...maybe others, I dunno. The MIST FPGA computer can run a ton of different 8 and 16-bit system images (here: https://github.com/mist-devel/mist-binaries/tree/master/core... ).
The Mega65 is particularly exciting on a few fronts, IMHO. The native feeling case and keyboard they have planned is probably the most exciting thing for me, but it's also based on a pretty modern FPGA, which should be able to emulate even late model AGA Amigas, among other things, should someone take the time to port the cores (MIST has cores for tons of stuff, so I would guess it'd be a reasonable thing for a small team, or even an individual, to tackle).
