I was wondering in the case of the other SC games as well if it would be possible to add 'supply units' to the game. I understand that the game's supply system is mostly automated, but perhaps units with similar qualities as HQs could be added. I was thinking about two types:
Supply depots: stationary (0 movement) land units that could be created by engineers or infantry (similarly to how ships create mines) and could have a constant 5-6 supply value. There would be only a pre-set amount of them available, and they would have minimal defense values so it would be very vurnelable to attacks. This sort of 'micro management' of supplies could make larger barren maps a bit more interesting.
Supply ships: vulnarable boats acting as 3-5 value ports when directly adjacent to a land hex. This way limited amphibiuos assualts could be attempted even without capturing a port of city right away.
It only would make sense, if you devide the headquarters into supply centers and generals, where generals are combat related and the supply centers give the needed supply to all of them. Then it makes sense for building some depots by pioneers, engineers, however. Or maybe you can raid some town or enemy depot for supply with some fast cavalry units, burning down some depots with spies.
There are a lot of options, one can imagine.
In case of naval warfare, this can be more necessary at the moment. So if you have larger naval operations or battles, there might be some flag ships/admirals or just some supply boats available. (like you had in wwII for example, oil tankers, special u-boats for supply, cargo ships ...).
Those are my small thoughts about your interesting input.