I apologise in advance for posting... (call it the 'pre-emptive whiners clause')
This game works in many ways on 'abstracted' concepts of real world actions, situations, elements etc. The supply system is no different but atm that 'limited' abstraction (ie capital central supply depot) is flawed and has issues.
I like the idea of user defined 'Supply Depots', supplies should not spawn at IC; why you ask, as IC is also an abstraction of relative industrial capacity in a region/province (example - how can you replicate in game something like German issues with ball bearing production and the allies persistent attempts at their destruction, you can't, but you can 'abstract' that in ways like IC bombing etc.). Supply spawning at abstracted IC negates concepts like shipment to distribution warehouses, civilian logistical supply network prior to becoming 'military supplies' (not to mention resistance forces, internal forces, inefficiency etc etc etc.. endless), bombing infrastructure and IC represents some of that abstraction sure but that really only covers mostly the abstracted production side of things
Supply Depots could (one conceptual idea, arguments welcome) could be linked to theatres/continents, example being Germany, one continent, two theatres = 2 Supply Depots which you can 'deploy'. They could only be strategically re deployable in some way which represents the 'massive' undertaking of moving an entire supply chain 'end point' for essentially an entire front to a new location. Supply depots can be bombed? sure, it would reduce the efficiency of the depot to supply fronts and receive supplies themselves, just like bombing planes, trains and ships, storage warehouses do not have some magical aura of invincibility.
The abstracted concept of overall military supply distribution could then be where you assign a supply priority to each depot and as such some 'magical' percentage of the overall supply system is assigned for delivery to that depot. Fighting on the Western Front and Russia is quiet?, change your distribution priority. The supplies delivered themselves can be abstracted via a (most likely convoluted) algorithm where distance from capital, infrastructure, techs, partisans etc influences 'actual delivered % vs defined supply %'. Moved your supply depot to occupied France for the Western Front/Atlantic Wall defense?, relying on a huge supply network stretching from Eastern Germany/occupied Eastern Europe to the English Channel, with resistance fighters, allied bombers, corrupt officials and such here there and everywhere, well what you send from your factories and such is not all going to be what arrives intact (but from there of course there possibly a reduced chance of loss, or maybe greater if in a more hostile region) inefficient, of course; but it gets the job done, and we are trying to take over the world here you know...
The supply map wont show this single transit line from capital to supply depot, why? cause the supplies are being shipped from everywhere, its 'conceptually abstracted' but of course from a supply depot to the troops on the line, well that would have some representation, but it might not have 'routes' more so than a 'sphere of influence' the further away the more 'accidents' that the delivering of the supplies can encounter en route (the usual infrastructure/partisan/occupied territory/terrain/attrition modifiers and such).
ok so i have probably rambled a bit... but i hope an idea is in there somewhere that could be developed.