So, from the software running on the machines point of view, the only difference is that the 68060 has floating point?
And an integrated memory management unit. Plus a superscalar architecture (though not pipelined, if Wikipedia is to be believed). The latter is not much of a problem since there never were any official Amigas coming from the main manufacturer with a 68060 installed, and it's just a means of speeding up execution rather than implementing a different set of mnemonics.
Personally, I think that if a more advanced make of CPU were to be coded into a FPGA, then it should be the one with the most informative exception handler stack frame (I vaguely recall that this began with the 68030, which could be made to recover from nearly everything you threw at it). A full implementation of the 68882 would be useful; I don't think the full 68851 is required and one can make do with the MMU-subset found in the 68030 and 68040. From the looks of the software-68000, it shouldn't be much work nor take much extra gates adding the instructions and abilities of a plain 68030 given that almost nothing changed in the register model save for the addition of proper support for longwords.