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I think a distinction needs to be made between systems where military leaders were elected by the whole polity, such as in the case of Republican Rome and Athens, and systems where soldiers elect their own superior officer.
 
That is the idea, but plenty of professional militaries, not least today's US Army shows that this idea of 'promoting on merit' does not mean more competent officers necessarily. You simply get structures of patronage, cliques and popularity contests within the military which then leads to people getting promoted based on their ability to play internal politics.
I think your answer, without attacking you, would be what a member of a professional military caste would claim as a defense against more democracy and against threats to his way of life.
All of the problems you mention would be significantly greater problems with elected officers. Promotion by merit at least means there are criteria by which performance is being measured. Now if the criteria are not being followed, or if the criteria chosen is not effective that's not a function of function. It's a failure of design.
You point to the US Army as an example and it's a fine one to use. The US Army, and pretty much all western armies use systems that turn out exactly the kind of officers that they are designed to turn out. That's why the US military functions as effectively as it does. Under the current structure of a 21st century tech heavy military effective administration (paper pushing and bean counting) is at least as important as trigger pulling. Is the system perfect? God no. But it's easily the most effective out there.
 
How common, historically speaking, has the direct election of military officers by soldiers (or other forms of military democracy) been? Are there any examples of this from ancient history in addition to more commonly known anarchist experiments?
I believe the Mongols did something like this.
 
I believe the Mongols did something like this.
If you go to tribal or early feudal structures, all leaders are elected.
It might that electibility is hitched to social status, but with the strong man rulers you have a strong undercurrent of voting with feet:
If the leader of the warband fails to provide plunder and glory his men will leave.
 
apparantly in roman legions the soldiers chose their own squad commander the "decanus"
 
That is the idea, but plenty of professional militaries, not least today's US Army shows that this idea of 'promoting on merit' does not mean more competent officers necessarily.
Not to forget that it's largely a "promotion on seniority" system anyway. Serve X years in rank, have done Y and Z, have qualifications A, B, C, move on to next level.
"Merit" usually amounts to "have this fancy medal for your special service", not to "this guy's great, let's put him in charge!"

I'd be dubious about how well a popularity based military force would work, too. I could imagine cases where it'd all fall apart. On the other hand, ideally in the modern world you have a highly motivated, intelligent group of soldiers somewhere in your army, and out of those "experts at warfare", well, why not have them decide who's going to lead their own groups? Seems unlikely they'd be so stupid as elect someone who gets them all killed just because he's a nice guy with good jokes.

Or maybe they would. Who knows.
 
where I think popularity based armies would fail is that it's leaders would put the survival of their men first over winning the battle/war lest they get replaced by another

while an opposing general with less regard for the comfort/survival of his men but more for overal victory would outperform him
 
I am dubious about that.
The International Brigades used to elect their own officers and of the many sins attributed to them military inefficiency was not one.
Eh. Let's not get carried away. The International Brigades were small formations, conspicuous in the media, that played a high-profile role in a losing war and which were primarily characterized by high morale. They suffered disproportionately high casualties, and the battles they fought in were usually defeats. They weren't exactly the Taman Guards.

Sovnarkom briefly promulgated the notion of elected officers in the Red Army starting in November 1917. After becoming War Commissar, Trotsky phased the practice out over a period of months, partly on the grounds of military effectiveness (because he wanted to reintroduce tsarist officers with more experience) and partly because he wanted to ensure that his orders were obeyed. He characterized the elected officers as little better than an armed mob, which I think is frankly the stronger argument for avoiding elected officers. Someone approved by their peers might or might not be a good and skillful leader, but the very notion of orders being a two-way street, in which the person giving the orders is chosen and responsible to those being given the orders, runs against the notion of a military hierarchy and of military discipline.

One can easily agree that patronage links and playing a political game are overly relevant to an ostensibly meritocratic military structure while simultaneously arguing that elected officers are still, in general, bad for armies.
 
I don't have any examples off hand, but most cases I've heard have been in the smaller tactical units, and in pre-modern times.
For example, a squad electing their squad leader. Rarely I've heard of the officers being elected without it being a total train wreck.