There is a distinct lack of fic that actually takes the whole "military organization" business into account, let alone the "giant alien robot military organization" part. Obviously I need to track down people like you who've been in the military and leech your brains :)

Actually, I've been accused of being too military, with the arguement that a lot of sources really don't seem much like a real military, but that... really varies strongly from canon to canon. Marvel included military style trials, court martials, and all sorts of similar details. Heck, at one point Hot Rod, while disobeying orders, thinks about how Kup will "probably have [him] drummed out of the Autobots for this." The idea that Kup has enough authority that Hot Rod would even think something like that was pretty odd in and of itself. (BTW, the story was "Ark Duty," which is also a canon example of Transformers being required to stand watch, since we're on the subject.. :) )

I don't know. I think military-ish elements are kind of neat, and don't really get why so many people don't like them. Granted, they do hold different standards and stuff, but still... *shrugs*