I'd like to see a blend of the old zone system mixed with the central strat targets. The central strat targets could resupply their respective sub-factories scatterred throughout the country. The sub-factories supply all friendly fields within a zone of influence. Captured enemy bases outside this zone will have to rely on player resupply or wait the full down time for an object to repair itself. Instead of having a bunch of factories tied to one zone base, I propose the allegiance of each sub-factory being tied to the ownership of their own field nearby (port, airfield, or v-base). If that field is captured, then the respective sub-factory will cease resupplying its default fields and will in turn start resupplying its particular zone fields owned by the possessing country.
Im torn about marshaling yards for trains and ships. If they handle transportation of supplies, the destruction of this facility would cause a strategic bottleneck. Why destroy one factory when you could destroy a marshaling yard and hamper the resupply of fields from all the factories? On the other hand, I greatly enjoy attacking and defending things of strategic value.