Natomi sounds kind of neat, but wouldn't a compatible OS on a say a G4 or some-such be better? Anyway, 68060 is faster than any classic Amiga.
Measuring performance is always tricky since you have the graphics co-processors to take into account, plus blitter, etc.
A base 68000 at 8Mhz is 1 Mip compared to 110 Mips for 68060 75Mhz.
But the original Amiga 1000 had graphics co-processors that could push pixels faster than the 68K could. So what is performance?
I agree that measuring performance is tricky as there are many different variables to consider so i think the way to approach this is to envision what it is going to be used for and start from there otherwise you may end up just confusing yourself

My 2 cents is not focusing on the technical aspect but more on what we will be using on the NatAmi and FPGA. Is there any classic software that can take advantage of all this power? I mean for an Amiga a 75Mhz 68060 is ultra fast but the 150 Mhz(?) NatAmi will make the 68060 seem slow.
Maybe another point i am trying to make is maybe the current performance measuring tools will not be relevant for the ng of classic hardware?