The CPU core is Mike's, and has separate instruction and data caches (much like the real CPUs), as well as other improvements in the bandwidth. As you know, I am a stickler for cycle exact emulation and compatibility, so the CPU core has full instruction set emulation and can be the exact same speed as a real A1200, or let loose! No FPU or MMU today, however, as pointed out that could change at any time with just a new core file. The FPGA Arcade Replay board has a pretty big FPGA on it, there is plenty of space for a large scale CPU replacement.
I really can't stand the 060. It breaks so many things, and when you kill all of the additional features that make it compatible, you end up with a CPU that is slower than a fast 040. But, Mike does have the 060 daughter board designed, so those that love the 060 will be happy I guess.