With all that, it has all the disadvantages of any large bureaucracy as well.  Cronysim, brown-nosing, advancement through sexual manipulation (in both directions) The Peter Principle, whatever; if it happens at any large corporation. large union organization or large State government organization, it happens in the military as well.

That 'authoritarian' base doesn't mean that leadership by example and other positive methods of motivation aren't also utilized.  They are in fact taught in all those required schools I mentioned.  

The bottom line is still "do it, go to  jail or get out", (like when the civilians impose social experiments on the trapped troops) but the other tools are there and used by successful leaders.