I dont usually agree with you Gruber but this is pretty bang on. Too much attention is paid to pitch counts and hard innings caps. Physical conditioning is the first consideration. I would further suggest that the things the average pitchers complain about and struggle with during a 162 game schedule should be the focus of any science that gets applied. Pitching a game in really cold weather, pitching off a cruddy mound, pitching an overly long inning, dehydration, nagging injuries, long road trips, pitching in the 76' sox jerseys and so on... all of these things will make a pitchers start more taxing than the mean.
With pitch and inning caps, coaching staffs are basically saying: The average pitcher takes an average amount of physical wear in an average start. Sometimes the wear is more and sometimes it is less but it averages out to 100 pitches and xyz innings cap.
It completely ignores the static physical fitness of the individual, the overall wear sustained, that human bodies heal at different rates, and that more physically fit bodies are less susceptible to injury.
To see teams announcing at the beginning of a season that a particular pitcher will have 150 innings cap is a joke. (looking at you 2011 blue jays)