The harnessing of the human body into a specific pathway for athletic or tactical production is a complex process. Personally, I think one that starts with examining human systems, first, then understanding the needs of the athlete. Ultimately, we should try and make sense of the performance continuum (prep, practice, performance) and how the related stress affects individual human systems.
How do stressors (external and internal) affect human systems and how does this play-out over the long haul? How does the individual athlete handle this or not handle this? For sure, strength and conditioning, and just as important, the expectations of training are stressors that can either predispose an athlete to regression and injury or enhance systems function and production. How do you know which path your heading down during training? That's a good question and one that has to be probed from an analytic standpoint within each situation.
Here's a list of human systems. Understand these first and how they work together, then try to understand how to better train the athlete.
Circulatory System (effectiveness of heart and vessels to circulate blood); Respiratory System (processes air); Digestive System (fuel and waste); Endocrine System (chemical communications system); Integumentary System (temperature regulation); Lymphatic System (defense); Nervous System (information processing); Muscular System (movement); Skeletal System (works with muscles to evoke movement/protects organs; Urinary System (filtration); Reproductive System (reproduction).