This is kind of in response to a few things, but here are some questions that help me form my perspective:
1) If I compare a 1.1 liter Ford Escort to a Formula 1 car, what is the most important difference that affects performance? The motor? The fuel? The tires? Fuel injection? On-board computer? Suspension? The exhaust? Unsprung mass? Transmission? Gear ratios? You kinda need them all, plus a whole lot more. How about a Winnebago versus an Indy car? Maybe the order changes, but you still kinda need them all. Sure, a powerful engine is important, as is the oxygen mixture but the tire manufacturer will remind you making the wrong tire choice can lose you the race. Luckily for running, by a long history of trial and error, we pretty much know how to train to get all the improvements we need, at the same time, without having to enumerate them, or decide the relative importance of a few of them.
1a) Building on the racecar analogy, the central governor might be the driver. With experience, and with feedback from his instruments, he learns how to drive to maximize fuel economy, maximize tire life, keep the engine from getting too hot, basically balancing maximizing performance with preserving the life of the car. You might also include the on-board computer as part of the central governor, controlling autonomous functions like fuel-air mixture.
2) Speaking of the role of coaches, which is more important for a coach to know? Physiology or psychology? I'm all for learning about exercise physiology, and it can be a fascinating area of discovery for those so inclined, but I'm not yet convinced that a deep or even accurate knowledge is required to be a good coach or athlete. Besides physiology, and training methodologies, running history, etc., a good coach must also be strong in soft human skills: motivation, inspiration, perception, feedback. Put another way, at the risk of revealing my age, who would make a better coach, Captain Kirk or Spock?
3) Richard, I haven't experienced your previous history, so you still have my benefit of the doubt. But regarding muscles, I don't get the impression that discussion of muscles have been pushed aside to make way for VO2max, LT, MLSS, or other aerobic, and anaerobic concepts. Over the course of my casual readings, I have seen lots of discussions regarding fast twitch fibers, slow twitch fibers, Type I, IIa, and IIb fibers, muscle recruitment, as well as concepts like specificity of training. Perhaps there may be specific concepts, like fiber contraction (?) that are untouched, but at least to me, I see muscles being discussed, as well as a lot of other things.
So far, my favorite post of this thread is HRE's "train the muscles, and everything else will follow". It's only a few words, yet upon deep reflection, says it all.