You can only do very simple designs in EEPROMs (like C64's PLA or Gary), no complex state machines like Buster, Agnus etc. are possible...
The C64 was so much simpler in design, there's no way to compare a redesign - definitely possible and has been done - to that of an Amiga. Of course it's possible but obviously it will not be done in the near future.
I habe a deep admiration for the guys having made UAE which must have been a tremendous amount of work. But what you are talking about is _hardware_ that not only has to function the same way as the original but even has to be compatible on pin level.
Come to think of it: when ferromagnetic logic circuits come out in 10? years, we can redesign a 'real' Amiga with ridiculous speed just with software tools - but then, who will want/need a 30 year old design?
