Ideal way to profile/performance-measure cipher implementations
It is unfeasible with newer CPUs to just count instructions, as newer CPUs can do multiple per cycle, and have multiple cores and likewise. 

Cycles per byte is the usual way to measure performance these days. 
Of course, to make it as fair as possible and comparable to others, the code is only ideally run on one core, turboboost and hyperthreading is turned off, etc.