First thing, I would do, is to make whole resource transportation system abstract. You would just add ships to area pools, together with escorts, subs, and raiders. That would at least allow AMCs chance for survival longer, than a week. Then if you have source of Unobtanium in Bora-Bora, you can use it, as long as path to Japan is clear. Without manually sending one single AKL to get it (and forgetting, that you sent it, 10 turns later).
The main problem is not absence of fuel for vehicles, but not including it in overall usage. 4Es should use at least 3 times as much supply, as they currently are. Does transferring plane from one base to another use supply? What about bulldozers? Those monsters drink as much gas, as tank, and I suspect, that Engineering Unit with Vehicles actually uses less supply, that one with comparable number of Engineer Squads.
And food. There was fraking famine in Bengal during war! Eisenhower wasn't in a hurry, to liberate Paris, because then he would have to feed whole city. And in-game, you actually gains enemy supply, when you win city hex from enemy. Just imagine, how much more supply you would need, if every liberated city would suddenly needed to be feed immediately.
And last important thing - wounded/sick/prisoners. You need to get them to safety to recover. Now, you just leave unit at rest, and two weeks later it is ready for another invasion.