The internal workings and valued personal traits of a "military organization" aren't a constant across the human history, though.
At some points, a model where orders are followed without question has been favored. At other points, the most effective military has been one based on loosely associated marauding parties or individual high-performance combatants who act in self-interest and without joint discipline. Some of the most potent militaries in medieval Europe were based on bought loyalty, requiring managerial skills of a very specific sort.
IMHO, there is no telling which sort of structure will best hold together a future military, especially in the curious circumstances of the Trek universe. Certain concepts of loyalty and hierarchy might still be useful, while others could bo counterproductive. Today, only the high leaders of nations have their fingers on doomsday buttons. In the 24th century, every infantryman essentially has a button of his own. Telling him to jump and not ask anything beyond "how high" simply might not be the psychologically, tactically and economically smart thing to do.
The lower-ranking soldiers of today typically perform duties that call for intelligence without morals or emotional weaknesses. Such a combination is not available anywhere in the known universe, so militaries pick intelligent people, deny them the application of morals, and tell them to suck in their emotions. But the fictional 24th century (and even the real 21st) is explicitly different from all the past of mankind: intelligence can be built into machinery without adding morality or emotion. In such a radically novel environment, the most efficient soldier might be the one that leaves intelligence at home and principally applies morals and emotions.
I mean, if Jellico wanted a four-shift ship, he could have pressed a button and the computers would have done that for him. Riker would be a pure dunsel in that respect, a man without any useful role aboard the ship. It is by no means impossible that the new important role for such a middleman in the 24th century military indeed is to provide maximal human inertia, necessary for the smooth functioning of an overautomated military machine.
It would be interesting indeed to see an organization based on such values, and exploring the delightful pros and cons of the exotique. Of course, Starfleet as portrayed is not as futuristic as it perhaps ought to be (or possibly indeed ought to, given that militaries are famous for their opposition to change), and "Chain of Command" thus plays out very much like a 20th century military confrontation between a competent commanding officer and an incompetent XO. But one should not categorically claim "militaries will always be the same" and fail to understand why they have been the same until now.
Timo Saloniemi