I'm probably not alone in giving a lot of thought to Kurage narrative play right now. One issue I've run in to is that I have no idea what the ranking system would be within the JSA. Would it conform to the present-day military? These seems to be the case, given that we see quotes and excerpts with ranks like "colonel" and "sergeant". What about the Ryuken-9? If they're based on Section 9 from Ghost in the Shell, their authority seems to be civil, but certainly they're used for military application. All of this is complicated by social and class standing within Japanese Culture too. How far can a Bushi rise, compared to a non-Bushi? Is there anything in their rank or title to differentiate them? I'd be curious to hear the ideas of others on this topic.
The Ryuken-9 fluff blurb in the JSA army pack book is actually pretty interesting. It's a military unit created to serve as a SpecOps force. They are a tactical asset to help shock troops get into the thick of things and do the work they need to do. Ninja clans helped provide instructors as the Ryuken Unit-9 required training in "[...]incursion, sabotage and early hostile contact as well as espionage and clandestine data collection". They report directly to JSA Spec Ops command but have a lot of flexibility in how they operate. "Ryuken enjoy a special status even among elite units, a position accompanied by what other officers see as an enviable degree of autonomy. However, many bushi look down on the Ryuken precisely because their operatives and officers are allowed to flout standard procedure and proper chain of command." So while they may not be chain of command, boot camp trained soldiers, they are no less a very much military unit rather than a civil one as their GitS parallel may be.
I think that the Bushi/non-Bushi difference is in what units you can enter. Bushi are Domaru and O-Yoroi, non-bushi are pretty much everything else (well, Ninja/Oniwaban/Shikami are a separate thing altogether).
There is also an element of 'service ensures citizenship' going on as described in the keisotsu fluff, and there are ways to advance up, as implied by the Tankos. So it seems likely it held a ranking system not too different from the Imperial Japanese army, given they still have generals and the like. I'd assume units would be divided based on caste, but there seems to be a system for advancement if you are capable and willing to risk your life for it.
I guess you need to be a Bushi to access to the highest ranks of the hierarchy (or at least, it must be easier for a Bushi to climb the ladder). At equal rank, I think a Bushi (O-Yoroi, Daiyokai, Domaru and even Tanko) will prevail over a non-bushi (Keisotsu, Aragoto) if there is a hierarchy problem (or the Bushi can always prevail if the cast is considered more important than the rank). Note that Ryuken Unit-9 have a great freedom of action and do not follow the usual chain of command (mostly like Kaizoku in fact). Ninja clans (Ninja, Oniwaban, Shikami) must have there own hierarchy and are sent on temporary assignment when working for the army. Kempeitai is kind like a parallel hierarchy, able to follow orders from higher ranked military but also able to take control when they think it's needed.
