From a pure energy standpoint, you want to compare how efficient the bow is in transferring energy to the arrow. That means you have to look at the force draw curve and consider the bow's total potential energy, then shoot an arrow to get the velocity of the arrow to calculate the kinetic energy in the arrow.
The parameters that the article uses, velocity/peak draw weight, will give very rough estimates of the bow's energy efficiency for they are nested in the potential energy/kinetic energy scenario I presented above. Those #'s will only give a rough estimate because the peak draw weight does not consider the shape of the force-draw curve. For example, a compound bow will have much higher potential energy then a recurve at the same peak draw weight and it is evident as to why when looking at the force-draw curves. I suspect the author chose to do it like that because that information is readily available whereas a force-draw curve is not.
Looking at velocity or FPS alone is, IMO, a selling tool and not a good comparative tool.
Hybrid Hunter - can you elaborate on the dynamic efficiency curve on your graph? I have not seen that before, what does it mean?