You benchmark them...?
Right, but that won't work in every situation now will it? Further, the benchmarks being used arguably could also fall into the same category of "not truly conveying useful performance metrics". Go look at any number of benchmarks posted here or elsewhere about particular CPU's, hell Jaguars, and you will find people picking apart the methodology and software used.
For instance, like Digital Foundry's "Next Gen" GPU comparison using off the shelf AMD parts that had their clock rates played with.
What I'm saying is, if we lament that 'using clock speeds and flops aren't legitimate indicators of real performance' then simply saying "well benchmarks" could fall under the same level of scrutiny.
I was inquiring if there were some kind of metric outside of flops or clock speed that could prove useful. Naturally we must accept the 'human' element in this situation and the intricacies of these architectures..