If you don't like napkin-back crayoning, skip to the next post.
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In the search for a more logical and effective Militia structure, would adopting a more flexible interpretation of what a "regiment" is be advisable - allow the retention of whatever benefits a certain identity and history confer, especially in areas where the local regiment has some standing, but without any sort of compulsion to maintain a full old-school RHQ?
If the actual strength is more-or-less battalion/company/platoon sized, then double-hat the appropriate OIC as Regimental CO - let the formation's HQ bodies fill the "RHQ" roles. If there's any requirement for admin/trg/log/whatever beyond what a particular formation can handle, fill that need with a cell distinct from the Batt/Coy/Plt structure - a cell that might be shared by several nearby units. Fine-tune the larger formation's command structure so whatever lieutenant colonels do exist end up commanding a battalion-sized collection of dispersed units - perhaps, in areas without a larger regiment, allow one of the "company" COs to be over-ranked. Over-man a bit as far as officers and NCOs, especially in smaller units, so a particular body deploying doesn't completely disable the unit - I'm assuming something like this already exists?
As far as headquarters - if the idea's to have a pick-up-and-go command cell for a brigade- or division-sized deployment, then don't lumber the HQ proper with militia housekeeping - peel that off as a distinct function.
Pros? Clearly defined roles. No rank inflation for the regiments, and a clear incentive for any units that, by virtue of local demographics, should be much larger, to determine what they're doing wrong. Perhaps a greater possibility of matching deployable roles for individual reservists with their rank and responsibilities at the home unit.
Cons? Howling from the National Union of LCols and CWOs, and everyone else with a vested interest in the current manning structure. Possible loss of experienced bodies. Likely public stink about "gutting defense," and the like. As it'd be (other than the loss of senior officer and WO billets) more or less a recognition of the status quo, not sure what else sucks about it - sure there's something.
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Oh - and make sure that any DND-maintained Militia infrastructure is seeing full use, whether by the primary unit, or by other CF organizations, whether recruiting offices, cadet corps, or what-have-you.
Speaking of that, why aren't CFRCs located in armouries, if there's one handy to a given area of interest?