Unfortunately it's just a game, & i feel it will be exploited has such until balanced, the new mechanics with industry does not favour combined forces, the safer option is to concentrate in one area and excel at it, having mutiple factories producing artillery/tanks/support equipment etc means having to keep varies branches of your armed forces supplied with different weaponry is not a luxury all factions can aford & if so in small amounts, and if just one of those branches aren't getting adequate weapons/supplies, then the unit has a whole isn't fighting at it full potential, not to mention they will potentially be subpar compared to those whom have fully invested into one area of there army compostion.
Although i believe there is more then one way to skin a cat, and i believe although daniel was using infantry only armies for the most part allowing his factories to easily concentrate and support his huge force, that if johan had chosen his battlegrounds a bit more wisely, he would have inflicted huge casualties. I also believe johan was having problems with dan's uboats that were kiting alot, perhaps a bit to much which would lock up an entire fleet for days at a time just to slip away, and thus the supply problems could have been put down to this aswell aswell as a lack of big enough captured ports.
Artillery is better were the fronts are narrow, and more firepower can be brought to bear, dan was using the brute force of his organization to push through, which would prove decisive once you have broken through, and after that the domino's continue to fall, resulting to being chased down & exterminated. Whatever Johan did was always going to be risky, since port striking would stop any invasion from succeeding & was the reason why players in HOI3 MP games would try to capture the biggest port but also have a bunch of ports already built and ready to deploy along with airfields & transport planes droping in supplies.
I believe the lastest Dev Diary hinted that occupied territory could have less supply throughput due to partisan actions and so forth, which would make sense, but the elephant in the room is the fact that brute german banzi charges with superior infantry equipment will win the day in most battlefield situations on a wider range of terrains aside from those with narrow fronts were numbers counts for little if not supported with proper combined arms.
I still personnally believe that had Johan after the loss of sweden chosen to make a concentrated push up through italy, used malta & africa to transport in supplies via transport planes along with the sea convoys, that an invasion force could have been maintained, and aided by offshore bombardment from the british navy aswell has gaining air superiority by upgrading & securing airbases in malta, sicily, corsica, sardinia, and supporting the invasion force in south italy pushing to rome by bombing infrastructure, and italian/german divisions in the north would have resulted in the least a tit for tat if not a slow grind forward & alot of dead for the axis. In HOI3 i never relied on convoy supplies alone, but had many transport planes that would be making sure that the boys on the front could still read there mail from home. Italy was a ideal fighting ground for causing daniel problems, and if it had been followed up alot earlier in the game, daniels efforts on the eastern front may not have gone according to plan, italy is the weak link in the chain, especially an ai controlled italy, and would have resulted in a logistical headache for daniel attempting to support italy. This would have made a later invasion of sweden/norway more successful which could have been carried by the US player to share the load, slowly exhausting daniels manpower fighting two fearious fronts, that would have then allowed for the eventual invasion of normany when only the childen & oldmen were left to man daniels alantic wall.